Nefarious

"What do you expect!? I'm a SUPERVILLAIN!!! Hahahahahahaha!"

- Dr. Nefarious

Doctor Nefarious was a robotic scientist who hated organic life forms, despite formerly being one himself. He was the archenemy of so-called "superhero" Captain Qwark, and later a recurring nemesis of Ratchet and Clank. Nefarious originally plotted to turn all organisms in the Solana Galaxy into robots. He was eventually defeated, but survived. Years later he began a new plan to gain control of time itself and remake history. He was again defeated, retreating into hiding after being rescued by his servant, Lawrence. He was then searched for all throughout the Polaris Galaxy by Galactic President Qwark (who took a great deal of credit for his defeat despite not being of much help to Ratchet and Clank). He later was forced to team up with Ratchet, Clank and Qwark.

Early life
"I always hated biology!"

- Dr. Nefarious

In high school, Dr. Nefarious attended the same 9th grade biology class with Copernicus Qwark where they were taught by Mr. Bozell. He had been constantly bullied and humiliated at the hands of Qwark, who was three times Nefarious' size and twenty-six years old at the time. His treatment included Qwark giving him wedgies, pouring lab beaker liquids on his head, cleaning chalk boards with his pants (while Nefarious was still wearing them), and being called "that freak with the headgear". Qwark apologised to him years later, and Nefarious stated that despite all Qwark had done to him in school, Nefarious had considered him a friend of sort. Because of this treatment and his difficulty with Biology, Nefarious would slowly come to despise anything biological. Later, he attempted a career as a scientist, only to be shunned and called insane. These experiences pushed Nefarious over the edge, and he set out to get revenge on all who had mocked him, especially Qwark.

Rise to evil
"I am the greatest genius the galaxy has ever known! You're no match for the likes of me!"

- Dr. Nefarious to Captain Qwark Dr. Nefarious eventually became a supervillainous mad scientist, while at the same time, Captain Qwark became a famous celebrity "superhero". The doctor started his campaign for revenge by creating the vicious Amoeboid creatures and launching an invasion on Blackwater City. After Captain Qwark defeated his "pets" and troopers, saving the burning city, Nefarious and his robotic servant, Lawrence, were forced to retreat in a rocket shuttle. Nefarious swore that he would have his vengeance "if it takes a thousand years!" as his ship took off. Qwark managed to grab onto the rocket and held his breath tight. He clung to the ship for six days, and it arrived at the doctor's base on planet Magmos. Qwark used a disguise to sneak into the base, unaware that Nefarious was watching him. The doctor commented that Qwark's poor disguise made him appear more stupid than ever, and ignored a solemn insult from Lawrence: "Even drooling imbeciles can achieve success in certain fields, sir. Mad science, for example..."

Dr. Nefarious decided to wait as Captain Qwark fought through his defences. The two soon confronted each other face-to-face on a narrow catwalk overlooking churning gears and machinery. Qwark seemed to have met Nefarious before, but he claimed they hadn't, trying to hide the truth from his nemesis. Qwark soon recognized the doctor from "Mr. Bozell's 9th grade Biology class," reminiscing on the "good times" of when he humiliated Nefarious, oblivious to how much his treatment had affected the doctor. Qwark said he should give Nefarious a wedgie "for old time's sake." While trying to grab him, he accidentally knocked him off of the catwalk into the spinning gears below, prompting Nefarious to scream Qwark's name furiously as he fell. Turning away from his nemesis' grotesque fate, Qwark then casually walked away, confident his rival was gone for good. As he made his escape, Qwark failed to notice a robotic hand pushing itself out of the rubble.

Dr. Nefarious had been forever changed into an advanced robotic being. This fit along well with his already immense contempt toward biological entities due to his miserable classes. Nefarious, much more powerful than before, resolved to continue his attempts to have revenge on the captain, and destroy all organic life in the galaxy, referring to organic life forms with the contemptuous name "squishies."

Vengeance
"Nefarious: This isn't over, Qwark! I swear, I will return some day to destroy you, and bring Metropolis to its knees!" Qwark: "Uh-huh... Just a word of advise Nefarious: Quit, while you're a head!' ''"

- Dr. Nefarious and Captain Qwark

A short time later, after Captain Qwark returned to his condo in Metropolis, Dr. Nefarious attacked the city with a massive horde of robotic locusts that consumed various forms of matter. He commanded his servants to bring him Qwark's head; however, despite the damage they inflicted on the city, Qwark eliminated the threat they posed and once again confronted his nemesis. Qwark and Nefarious promptly battled in close-quarters one-on-one combat. Despite the vast array of superpowers he had been granted from his transformation, Nefarious was defeated once again, greatly damaged and left as a disembodied head (which is ironic, as he had hoped to have Qwark's head). Qwark threw Nefarious' head in a trash can as he screamed his revenge. The captain was then suddenly attacked and knocked out from behind by Lawrence, who had returned to aid his master after picking out torture chamber curtains. Nefarious urged Lawrence to hurry them away from Kerwan with Qwark in tow. They then imprisoned him on Nefarious' Ice World.

Captain Qwark, still asleep, had a brief dream, but soon woke up shocked. He asked where he was, locked in a cage descending from the ceiling by a chain. Dr. Nefarious, still a mere head held by Lawrence on a silver platter, explained "You're in my secret prison, awaiting the most ingenious and depraved punishment I can possibly imagine!" The doctor and butler then left for Nefarious' massage, which Lawrence was less than cheerful about. Qwark managed to escape the prison, accidentally setting off the alarm and causing acid to rise from the floor. Making it out, he retreated to his hideout on the Thrann Asteroid, where he hid until Nefarious allegedly disappeared. In reality, he was being repaired by Lawrence and was given a new body. However, Lawrence mistakenly attached Nefarious' head backwards. Nefarious could not see his arms, and looked down, asking frantically "Whose butt is this?" The doctor angrily screamed at his apologizing butler, causing himself to malfunction. The doctor was completely frozen as his brain began to pick up signals from a soap opera, Lance and Janice. Lawrence said that he would need to repair the glitch, then chuckled and said that it would be done "one of these days." However, the glitch never got fixed because the only highlight of Lawrence's days at work was getting to slap him so that he would unfreeze.

Age of Robots
"Robotic citizens of the Solana Galaxy... the hour of your liberation is at hand! Too long have we robots suffered under the bigotry, the stupidity, the squishiness, and foul stench of organic life forms! Soon, all robots will bask in the liberty and equality of my benevolent, iron-fisted rule! And, as for you filthy organic life forms... You can look forward to being disintegrated! (Laughs manically) That's all for now..."

- Dr. Nefarious' message to the Solana Galaxy

Ten years later, Dr. Nefarious started an entire public campaign to rid the Solana Galaxy of organic life forms. Nefarious formed an alliance with the Tyhrranoid race, who served the doctor as his personal army, gullible and oblivious to the fact that they were organic life forms. The heroic duo, Ratchet and Clank, saw a news report detailing an attack on planet Veldin, Ratchet's foster home, by Tyhrranoid soldiers. Dr. Nefarious was believed to be the attack's mastermind. Later, on the Starship Phoenix, that fact was confirmed; Captain Sasha, Ratchet and Clank were listening to a distorted distress call from the Galactic President, who was requesting assistance to stop a Tyhrranoid invasion force on the Capital City of Marcadia. The message was then completely cut off by a galaxy-wide broadcast from Nefarious, who made his introduction to his new enemies from his office on Aquatos.

In the message, the diabolical doctor dramatically announced his entire plot, while Lawrence acted out his words so that the deaf could understand. Ratchet and Clank then managed to stop his attack on Marcadia. Later on, Clank explored Nefarious' Office in his "impenetrable" secret base on Aquatos, and found out that he was a huge fan of the Secret Agent Clank Holo-Vision series, having the entire episode collection, which disturbed Clank. Lawrence informed Nefarious of the break-in on his ship, the Leviathan, while he was watching Secret Agent Clank, which the doctor referred to as his "work." This news outraged the doctor, and caused him to crash and pick up soap opera signals again. After being smacked back to normal, he ordered Qwark's Q-Force, which Ratchet and Clank were a part of, annihilated. The team's next mission was an attack on the Tyhrranoid homeworld, Tyhrranosis, where Ratchet and Clank defeated the Momma Tyhrranoid.

Biobliterator
As the Q-Force listened to Ratchet's recount of the fight on the Phoenix, Dr. Nefarious and Lawrence transmitted to them via hologram, mocking them. The doctor declared "I could obliterate the lot of you, and they wouldn't even mention it in Supervillain Weekly!" Nefarious was referring to a holo-vision show that he was often interviewed on about his evil schemes. He then said he had "far grander plans" for 'Agent' Clank. He then maniacally laughed, trying to end the transmission with a triumphant, intimidating appearance. The hologram remained on, followed only by awkward silence. Nefarious then had to whisper to his butler to turn off the transmission. Lawrence did so, having ruined his superior's moment with his spiteful sarcasm. Ratchet had Big Al trace the signal of the message back to the source. He showed them that it came from a facility on planet Daxx. He also patched through a video from Supervillain Weekly of Nefarious and Lawrence at the facility.

The doctor and butler were being interviewed about Dr. Nefarious' new top secret superweapon constructed on Daxx. The interviewer said "Dr. Nefarious, we've all enjoyed your past work, but how do you respond to critics who say your latest galactic schemes are just more of the same?" Nefarious responded with a loud "I will annihilate them!" Lawrence could not comment with any details of the superweapon, but changed the subject and said "We do, however, have a lovely view of the ocean at sunset." Nefarious happily nodded in agreement at this, taking a bit away from his evil image. The announcer finished the broadcast with "Is Dr. Nefarious poised on the brink of galactic domination, or is this 'superweapon' just the latest in a series of maniacal pipe dreams? Stay tuned for more, from Supervillain Weekly!" Ratchet and Clank then explored Daxx, and found out the device was the Biobliterator. Nefarious had removed all data on the device, but it was deciphered that it had been transported to the Obani Moon System.

Courtney Gears
It was also revealed, through the Anti-Squishy Music Video, that robotic pop star, Courtney Gears, was in league with Dr. Nefarious. He used her music as propaganda to spread his vendetta against organics, being a big fan of hers. Gears was apparently in love with Nefarious, giving him the pet names like "Snooky Wookums," though this annoyed him greatly, and he valued her as an ally, but kept their relationship professional. While on Holostar Studios, Clank needed to film a Secret Agent Clank scenario, with Gears as a character. After the shoot was over, he asked her what Nefarious was planning, and she was able to capture Clank by knocking him out. She then contacted Nefarious, who was greatly annoyed by her reference of "Snooky Wookums," and told her to bring him 'Agent' Clank. In an office Nefarious had commandeered at the studio, he tried to turn Clank over to his side, as he was a fanatic of his series and believed it to be real, following his 'missions' from the beginning.

The doctor even rejected Clank's assurance that the series was just an act, calling the statement "Lies! Squishy lies!" His anger caused him to freeze and pick up soap opera signals again. Gears had to smack him to get him back to normal. When Clank refused to join, Dr. Nefarious decided to replace Clank with a doppelgänger, Klunk. Posing as Clank, he told Ratchet that Nefarious was aboard the Leviathan. Later on, Nefarious launched an attack on Blackwater City, which was also stopped by Ratchet. He and Klunk then went to Obani Draco, Gear's headquarters. Ratchet was shocked to witness a recording from the testing lab for the Biobliterator, which had since been transported away from the moon: Gears had used the machine to transform Skid McMarx into a robot. Ratchet thought this impossible, but Klunk said "Not for Dr. Nefarious..." The Lombax then defeated Courtney Gears in her studio, and received a transmission from Captain Sasha.

Leviathan trap
Dr. Nefarious' starship, the Leviathan, had been tracked to the Zeldrin Starport, where it was refueling. Ratchet, Klunk and Qwark then met up to infiltrate the ship. As soon as they arrived on board, Klunk secretly received a message from the doctor to lure them to the bridge. They soon located Nefarious, greeted casually by Lawrence. Commenting that Qwark had gained weight since their last encounter, Nefarious was angered by Qwark saying that "Courtney Gears didn't seem to mind." He went into yet another crash sequence, prompting Lawrence to happily smack him across the face. Nefarious declared he would have the last laugh, as he lured Qwark and Ratchet so that he could witness their demise. He then activated the self-destruct for the ship and commanded Lawrence to teleport them away. Lawrence left himself, leaving Nefarious behind. The doctor was not amused by this, and was teleported out moments later after shouting to him. While Ratchet and Klunk escaped, Qwark seemed to go down with the ship, trying to grab something.

Metropolis battle
After Captain Qwark's funeral, Ratchet deduced that Dr. Nefarious was planning on making good on his vow to destroy Metropolis, which was shown from years earlier in the Qwark Vid-Comic, Deja Q All Over Again. He traveled to Kerwan and took part in the large-scale battle, searching for Nefarious. Meanwhile, watching the battle from a Hover Train, Nefarious showed Clank Klunk's transmission of Ratchet's actions, meaning he could track the Lombax. Nefarious found the whole prospect delightfully amusing, laughing diabolically and trying to get his butler to go along with him. Lawrence merely said "You put the wit in 'twit', sir." Taking this as a compliment, Nefarious continued laughing happily. He declared that it would be the dawning of a new era, all thanks to his years of secret plotting and patience with many disappointments. The doctor arrogantly rebuffed Clank's confidence in Ratchet's abilities, claiming that Ratchet would be killed with Clank having a "front row seat."

As Ratchet traversed through his forces, Dr. Nefarious revealed the Biobliterator itself. He tried demonstrating its ability to transform any organics into robots, demanding the activation device from Lawrence. Proclaiming the new "Age of Robots," the doctor pressed the remote; however, it instead turned on a video recording of his Galactic Idol audition. His butler had given him the wrong switch, angering him and causing him to furiously knock him over. 'Apologizing,' Lawrence gave his superior the correct remote and assured him he could continue. Looking away in case it was another error, Nefarious pressed the activation device, delighted to see it successfully activate the Biobliterator. As he laughed evilly, the machine rose up, transforming his remaining Tyhrannoid soldiers into Robonoids. Ratchet fought through these new metallic enemies and soon found out that the robot at his side was Klunk, Clank having been captured by Nefarious, who casually waved at Ratchet when he reached the Hover Train.

The doctor mocked Ratchet before leaving with Lawrence, laughing so hard that his sides began to ache from all his laughter throughout the day. However, he did admit that Ratchet was a far better adversary than the "imbecile" Qwark was. Ratchet fought Giant Klunk on the Hover Train and managed to defeat him and save Clank. Nefarious then launched a Robonoid attack on Aridia, which was again stopped by Ratchet and Clank. Meanwhile, Nefarious piloted the Biobliterator to different planets across Solana and turned many into robots, making it look like there was more than one due to the speed of the attacks. Ratchet and Clank went to the Crash Site of the Leviathan, thinking that whatever Captain Qwark had tried to grab as the ship exploded may have contained some sort of clue. They discovered that Qwark had gotten away from the ship's destruction in an escape pod and went into hiding for some reason. They also retrieved a data disc, which is what the captain had been trying to get. Back on the Phoenix, Ratchet gave Al the disc to decode, which would take him some time.

Qwark's disappearance
Al also gave Ratchet the secret final issue of the Qwark Vid-Comics, The Shaming of the Q, which revealed Captain Qwark's capture at Dr. Nefarious' Ice World and escape to his hideout on the Thrann Asteroid. Ratchet resolved to travel there and confront Qwark on his disappearance. He expressed to Clank his suspicions that Qwark was in fact working with Nefarious. Clank found this hard to believe, but Ratchet reminded him that during their time knowing the captain, he had been rather antagonistic towards them, teaming up with Chairman Drek and orchestrating the Protopet disaster in the Bogon Galaxy. After confronting Qwark on the truth of his disappearance, Ratchet discovered he was simply trying to hide from Nefarious' attack on the galaxy, showing his utter cowardice. Ratchet, Clank and Skrunch then left him in disgust. It was decided that they would defeat Nefarious without him, though their words about the situation caused Qwark to rethink his position.

Battle plan
Ratchet then received a distorted message from Captain Sasha on the Phoenix, which was under brutal assault from Dr. Nefarious' troops. She told them that whatever was on the disc Captain Qwark had found had Nefarious worried, and he was prepared to destroy the team to get it back. Ratchet hurried to the ship and fought past the doctor's attack force. He reunited with his comrades on the bridge, and thanks to Al successfully decoding the disc, they found Nefarious' entire battle plan to attack planet after planet all over the galaxy, creating an entire population of robots in Solana. The doctor was confident that the Q-Force would never be able to stop the Biobliterator. Sasha told Ratchet that the machine was recharging at a base on Koros. Ratchet was determined more than ever to stop Nefarious after he learned that his next target was Veldin. After the duo fought their way into the base, Clank used the Nefarious BFG ion cannon to destroy the Biobliterator while Nefarious was screaming furiously from a video screen.

Captain Sasha then contacted the duo, informing them that Al had finished decoding the disk. It was discovered that Dr. Nefarious was preparing to use his second Biobliterator, more powerful than the first, and it was being fueled on Mylon, his master control center. Ratchet and Clank were able to defeat the last of Nefarious' Robonoids and approached him at the Biobliterator's fueling dock. As they got to him, Nefarious and Lawrence teleported into the Biobliterator, which flew away, done fueling at the last moment. Nefarious laughed maniacally as his machine flew away, confident his plans would succeed. They pursued him to the Launch Site, where the doctor had already initiated the launch sequence. Ratchet confronted Nefarious as he operated the take-off procedure from a console that had a green color scheme and dome reminiscent of the doctor's own. Nefarious was rather annoyed to see Ratchet interfering with his plans once more, expressing how the "miserable rodent" would pay for his "insolence."

As the doctor furiously monologued, Ratchet threw his wrench at him. Dr. Nefarious barely managed to dodge the wrench as it crashed into and destroyed the console. Ratchet declared that Nefarious' flight was canceled, and the enraged doctor called Lawrence to his side. Nefarious waited impatiently, continuing to shout his butler's name, as he would not appear. A hologram of Lawrence then answered, to which Nefarious ordered Ratchet's annihilation. The hologram revealed itself to truly be Lawrence's voicemail, asking for a name and brief message before vanishing. Nefarious then said, frustrated, "Fine. I'll do it myself."

Showdown with Ratchet and Clank
Dr. Nefarious faced off against Ratchet and Clank in close-quarters combat, proving to be a formidable adversary thanks to his powers. He soon decided to fool Ratchet into believing he had won the fight in order to give himself time to escape. He knelt down on the ground, faking coughs and whimpering, and declared that he had no choice but to throw himself on Ratchet's mercy. The Lombax, initially shocked, then triumphantly stated that the doctor's reign of terror had ended and fell for the ruse. Ratchet did not expect Dr. Nefarious to rise from the ground, activate a forcefield around himself, and fly away. Nefarious shouted "Sucker!" to his foe as he escaped, laughing mockingly. Angered by this, Ratchet pursued Nefarious to the battlefield where his remaining troops and the floating Biobliterator waited. With help from the Galactic Rangers, the duo broke the doctor's final defenses and confronted Nefarious beneath the Biobliterator. Despite exhausting almost all of his abilities, Nefarious was bested in combat and knocked to the ground.

Dr. Nefarious again called Lawrence to his aid, who actually appeared this time, dressed in a rockstar costume. The butler was reluctant to follow Nefarious' orders, having been preoccupied with guitar practice, which he clearly saw as more important. Picking himself up and dusting off, the doctor ordered his butler to "Begin the transformation!" and shouted at him when he continued to be distracted by his guitar. At Lawrence's pressing of the activation device, the second Biobliterator changed into an immense mechanoid. Nefarious broke into a diabolical laugh as he and Lawrence teleported to the cockpit, ready to depart and bring about the mad scientist's Age of Robots; however, as he began firing at Ratchet and Clank on the ground, he was shot at by Captain Qwark, who arrived on the scene in his own shuttle. He had decided to come out of hiding to help defeat his nemesis, wanting to be a true hero. Distraught at this, Nefarious yelled in frustration "No! I don't believe it!", and Qwark replied with "Believe it, toasterhead!"

Ratchet, Clank and Qwark managed to defeat Dr. Nefarious in the air and destroyed the second Biobliterator. The head of the mechanoid landed on the battlefield, and Nefarious was greatly humiliated by being defeated at the hands of "squishies," believing he would never live it down. The cockpit's computer announced that the reactor would detonate in sixty seconds. Nefarious then bluntly told Lawrence to engage the teleporter. Lawrence asked him to specify a destination, and Nefarious said "Who cares? Just get us out of here." The computer then said time was up, and he shouted "What!? That wasn't even close to sixty seconds!" The computer childishly responded with "Buh-bye!", prompting a terrified expression on the two. Right before the Biobliterator's head exploded, Lawrence teleported them away in a panic, having no time to pick a destination for them.

Stranded
"Thanks to you, and your dimwitted friend here, I found myself drifting through the cosmos! Have you ever spent time on an asteroid? It's surprisingly BOOORIIING! Nothing for a villain to do but dwell on his failure!"

- Dr. Nefarious to Ratchet and Clank

Dr. Nefarious and Lawrence were stuck far away on an asteroid in space, unable to teleport to another planet, as they were well out of range. According to Lawrence, it would be five or ten thousand years before something came for them to teleport to. Nefarious shouted angrily in disbelief, and then sat on the ground. He then said "Now what?" as his butler looked at him. Lawrence asked him "I don't suppose you can play drums?", wanting someone to go along with his guitar to pass the time. Infuriated by this ridiculous question, Nefarious screamed at his butler. While Lawrence spent most of their drifting playing his guitar, Nefarious simply sat thinking over and over about his failure, which would continue to haunt him.

While stranded Lawrence told Nefarious that they were coming within range of a space station. Unfortunately, it exploded mere minutes before they passed it. Furious at Lawrence, Nefarious shouted his butler's name at the top of his lungs, only for another transmission of Lance and Janice to play in his head.

The two were still forced to aimlessly drift through space. After some time, the asteroid drifted to the Polaris Galaxy. In Polaris, the two seemed to briefly come upon planet Mukow, as the doctor's wallet was found and held at a concession stand.

The pair also spent much time drifting through the Breegus System, even being spotted by space pirates in the Corvus Nebula while Dr. Nefarious was having one of his malfunctions and screaming at Lawrence, playing an episode of Lance and 'Janice. Despite Lawrence's claim of the time it would take for them to find refuge, the rock picked up speed and turned into a ball of fire after drifting to planet Zanifar. It crashed in the Tobalia village of a local Fongoid tribe, forming a crater, which was barricaded. Nefarious and Lawrence sought refuge with the tribe, arriving as they were in the middle of celebrating spring break.

Copied
During Secret Agent Clank, Klunk made a copy of Nefarious which had his abilities and was programmed to obey Klunk. He was destroyed by Clank in the final confrontation with Klunk.

Arrival in Polaris
"Then, one day, the Fongoids saved us. But still, faliure BURNED inside my circuitry! How could I have been defeated by the likes of you? Why had the universe been tipped in your favor? I embarked on a crusade into the inner recesses of, what you call, the soul."

- Dr. Nefarious to Ratchet and Clank

While living with the Fongoids on Zanifar, Dr. Nefarious tried to decipher how he could have lost everything he had worked so hard to accomplish to his enemies. He even spent one night twitching and cradling himself in a darkened room after drawing several pictures of Ratchet and Clank on the wall, crayons clenched in his hand and mouth. Nefarious decided to go on a spiritual journey to find the answers he sought. He spent his time on Zanifar studying Fongoid meditation, attending numerous anger management classes, and dabbling in yoga. Eventually, he went on a spirit walk on planet Quantos. It was here that he learned of the mystical Zoni race, who were in charge of protecting the universe and keeping it in balance. He also discovered their ultimate creation: the Great Clock, a facility in the center of the universe (give or take fifty feet) which kept the flow of time and effectively acted as the cosmos' greatest contingency plan. Nefarious secretly plotted to gain control of the clock to rewrite history, making it so no villain would ever go through such a humiliating defeat as he did, and so that heroes would always fail in their righteous endeavors up to the present. With this plot, he temporarily put aside his organic life form vendetta, again working with "squishies" if it suited his plans.

Dr. Nefarious fooled the Fongoids into believing that he was loving, kind being, and they came to worship him. Canceling their spring break, he used them as a task force to help construct the Tombli Outpost in their Tobolia valley, which he used as his temporary base of operations. It would go on to be the primary manufacturing plant for his new army of starships and Nefarious troopers. He then made new allies with other villains who also wanted to use the clock for their own ends. He hired Terraklon mercenary and former assassin, Lord Vorselon, to serve as field enforcer of his troops. Vorselon had lost his body in a battle against the Drophyds on Zaurik, being confined to a cyborg suit. In addition to bolt payment, he was promised to have his original body and glory restored with the clock's power. The doctor also got into contact with Pollyx Industries and formed an alliance with the Terachnoid CEO, Pollyx, who signed his corporation and most Terachnoids in an exclusive contract to work for the doctor, having access to valuable Zoni technology and knowledge. With assistance from the labor and resources of the Fongoids, Pollyx Industries worked toward building the Nefarious Space Station, which would be the doctor's headquarters.

As his station was under construction, Dr. Nefarious kept his evil activities in the Tombli Outpost secret from the Fongoids and waited to reveal his devious schemes to the rest of the Breegus System. Using Pollyx's holdings, he managed to contact the Zoni leader, Orvus, requesting an audience with the fellow scientist. A being of etiquette, Orvus honored the seemingly friendly robot's wishes and traveled to the outpost. He was then taken by surprise and imprisoned.

Finding Clank
"Remember when I told you where your new master was and you kidnapped him? Ha, Ha, priceless!"

- Dr. Nefarious to the Zoni As Lawrence stood by with Pollyx and a Protomantis, Dr. Nefarious interrogated Orvus about getting inside the Orvus Chamber, the Great Clock's control room that commanded the flow of time. He tortured Orvus when he repeatedly refused, having his machine, the Hypersonic Brainwave Scrambler, blast him with its sonic energies, a vulnerability of the Zoni. Nefarious failed to heed Orvus' insistence that time was not to be tampered with as he continued to grow weary of the torture. Nefarious shouted at Pollyx when the interrogation continued to fail, as Pollyx was scanning Orvus' brain for the key to the chamber but could not find it. Pollyx believed that the Zoni had erased his own memory, and Nefarious gave him one final chance to tell him how to access the chamber. Orvus again refused, and Nefarious furiously clenched his fists over his head before again signalling his device to blast him. Orvus held off the blast, saying that the only one who would enter his chamber was safe, far from the doctor.

The growing light of the held-out beam made Dr. Nefarious and all present cover their eyes. Orvus then dissipated in a flash, and Nefarious frantically asked where he went. Unable to deduce where Orvus had gone, Pollyx still managed to pull up an image from his memory scanned before he vanished. The image was schematics of Nefarious' old nemesis, Clank. It was revealed that he was in fact Orvus' heir and the key to entering the Orvus Chamber. The doctor planned to get a hold of Clank through the Zoni, who were still unaware that the doctor had kidnapped their leader. Nefarious contacted the Zoni and offered to help them find Orvus' heir so that they could bring him to fulfill his destiny. When Ratchet and Clank came to Polaris and defeated Emperor Tachyon and his Empire and, Nefarious led the Zoni to their new master. They aided Clank in the journey to vanquish the Cragmites, appearing before him on occasion. They eventually brought him to the Great Clock to understand his purpose.

Ratchet soon set out to find his dear friend, unaware of Dr. Nefarious' new schemes. After battling space pirates and learning a bit about the Zoni through the travels of Captain Darkwater, Ratchet retrieved a Fulcrum Star and used it to power an Obsidian Eye on planet Merdegraw. With it, he traced the Zoni and Clank's location to the Breegus System and managed to catch a brief glimpse of the Great Clock during a visit from Nefarious; Clank's logic and memory seemed to be dysfunctional, and the Zoni relied upon the doctor to repair him. He then appeared, slightly silhouetted in the doorway of the mnemonic station where Clank was being held. Ratchet watched as he walked down the stairs, being revealed in the light bit by bit, but then slipped on a feather duster left carelessly on the floor by his butler, which caused him to fall down the stairs screaming. Fully revealed, Nefarious was shown angrily shouting at Lawrence once again.

Ratchet and Talwyn Apogee were then given coordinates to the Breegus Nebula, the entrance to the system where Dr. Nefarious had resurfaced, as the signal was lost. Ratchet vowed to rescue his friend and defeat Nefarious once more as he and Talwyn departed from Hoolefar Island. While Ratchet took off in the Aphelion beside Captain Qwark, who was eager to get back into 'the hero business' after doing some film acting, Talwyn stayed behind, warning Ratchet that where he was headed was home to a great deal of mercenaries. It was these very guns-for-hire that would assist in Nefarious' new plot and prove to be a large obstacle for Ratchet.

The Great Clock
"Patience, Lawrence. We have all the time in the universe..."

- Dr. Nefarious "In which the heroes ALWAYS Lose!" -Nefarious to Ratchet

When the Nefarious Space Station was eventually completed, Dr. Nefarious revealed his true villainous colors and imprisoned the Fongoids in work camps around the Tombli Outpost. The base was fitted with much security after the doctor went to his new station, a statue also being made of him before the entrance to the outpost in a triumphant stance in front of the asteroid he had drifted on for so long. It was at this point that the doctor's evil campaign was made fully public. He took control of the Bernilius Sector where his station was located, and further imposed his will on the Phylax Sector, Vela Sector and Corvus Sector thanks to the influence of Lord Vorselon and Pollyx Industries, sending fleets and satellites out to keep the system under secure watch. With Nefarious' army on the rise, an exiled Lombax freedom fighter, Alister Azimuth, began battling his forces to try and save Polaris. Through his fight with the elder general, Nefarious discovered the full history of the Lombaxes and Ratchet.

For over a year, as his henchmen enforced his will throughout the Breegus System, Dr. Nefarious and Lawrence continued to visit the Great Clock and keep a false alliance with the Zoni, using the pretense that he was repairing Clank as a facade to keep their trust. He was often opposed by the facility's Junior Caretaker, Sigmund, who tried to save Clank, knowing full well that all Nefarious wanted was the Orvus Chamber. Each time the doctor tried unlocking Clank's memory banks, the neural safeguard would lock him out. His constant failures, along with his overall annoyance of pretending to be friends with the Zoni, frustrated Nefarious greatly. During a visit, he mocked the unconscious Clank floating in the mnemonic station, saying "Ah, my arch nemesis... Not so smart now, are you?!" and banging his head. Lawrence then informed his superior that the Zoni had been inquiring about their progress, angering the doctor.

The Zoni then entered the room, reminding Nefarious that he must fix Clank. He assured them that he was doing his job and again entered the brain's system, trying to arrange Clank's memories correctly to see into his subconscious. He was once again locked out, nearly having a breakdown in his frustration. Nefarious then exclaimed "It's in here, Lawrence! Somewhere in this brain lies the key to the Orvus Chamber!" Upon hearing this, the Zoni firmly told Nefarious he was forbidden from accessing the chamber, as it was only meant for the Senior Caretaker of the Great Clock, which was Clank. His insistence to no avail, Nefarious betrayed them and activated the Hypersonic Brainwave Scrambler. It's sonic wave attacks forced the Zoni out of the room. As Nefarious laughed maniacally, the room went completely dark; a black-out had occurred in the clock, as the equipment was especially susceptible to sonic weaponry, which Lawrence apologized for not mentioning earlier.

The back-up generators restored power seconds later. When the lights came back on, Dr. Nefarious saw that Clank had managed to awaken from his slumber and escape in the darkness. Nefarious angrily ordered Lawrence to stop him as he fled. Over the loud speakers and appearing on large projection screens beside Lawrence, Nefarious asked Clank to come back so they could discuss things "robot to robot." The doctor's troops, meanwhile, were firing at the fleeing Zoni and Clank, causing much damage to the clock in the process. Lawrence informed Nefarious, who frantically told his troops he wanted to Clank alive. The robot soldiers did not obey Nefarious' commands, as damage had been done to their hive mind in the ensuing chaos, and Lawrence needed to reboot them. They also detected that Sigmund was trying to aid Clank's escape. Nefarious ordered Lawrence to reset the locks and track the "meddlesome" caretaker's location.

All the while, Dr. Nefarious' troops were chasing after the Zoni, who continued to flee and evacuated the clock. Upon hearing the dropping number of Zoni from Lawrence, Nefarious told them to come back, exclaiming that he was just kidding, and joking about how they had kidnapped Clank thanks to him. When Clank knocked over a neatly stacked pile of crates belonging to the doctor at Sigmund's behest to get ahead in his escape, Nefarious threatened Sigmund, saying "When I get my hands on you, I'll rip that dome of yours off, and pull out your brain with my bare hands!" Lawrence sarcastically complimented the doctor's "tough talk," truly not finding it intimidating at all. While Clank escaped his troops, Nefarious told Clank he would not be able to fly to Polaris and that if he wanted to keep his brain, he should surrender. Sigmund's location was eventually discovered to be in a broom closet, and Nefarious had him locked off from Clank for the time being. Clank then stopped at a balcony, with no other escape. Nefarious and Lawrence confronted him on the platform, where Nefarious dared him to jump, and then laughed mockingly. Clank then asked where his old enemy had taken him. Nefarious showed Clank his home, the Great Clock, and described its location and history.

Clank wondered what lie Dr. Nefarious had told the Zoni and believed that the doctor had sought vengeance. Nefarious found it odd how Clank thought he went to all the trouble he did of taking over the clock for mere vengeance, and said "They say I'm ego-maniacal". He then said that "it's...all in the past." He had Lawrence use the orb of gratuitous immobilization to freeze Clank and knock him out. Lawrence suggested they use the Mnemonic Station again, but Nefarious said he had better plans. When Lawrence questioned this, he said "Patience, Lawrence. We have all the time in the universe..." Nefarious then returned to his space station and began rehearsing an original play he wrote: Night of the Living Squishies. He used his robot troops as actors to practice scenes, and gave out several script books. He had his soldiers line up at the door outside his personal chamber, where he was rehearsing scene four of act three. In the scene, Nefarious held Captain Qwark at gunpoint while the captain tried to capture him.

However, Nefarious' rehearsal was repeatedly halted when he accidentally killed the troops playing Qwark with the pistol he was using, which was supposed to be unloaded. The more troops went in to attempt the part, the more of them were killed, and the more the line outside shook with fear. Meanwhile, back in the Great Clock, Sigmund was teaching Clank things about traversing through the security systems and dealing with enemies. They encountered the Hypersonic Brainwave Scrambler, which had been left loose in the clock, crashing into and damaging much machinery even after the Zoni it was chasing had escaped. Upon destroying the sonic device, Clank and Sigmund continued onward through the clock, but were silently being watched by Lawrence, who had remained in the clock to keep an eye on them on Nefarious' orders. He contacted Nefarious via hologram, inadvertently interrupting yet another one of Nefarious' rehearsals, upsetting the doctor.

Lawrence reported to him that Clank was en route to the Orvus Chamber. Dr. Nefarious laughed with delight at this news, as he wanted Clank to lead him directly to the chamber. Nefarious prepared to go back to his play, but Lawrence informed him of another matter, showing him a video camera on Vorselon's warship of Ratchet and Qwark rescuing the locked up Fongoids they had come to the Breegus System and were fighting the doctor's forces to try and rescue Clank. This revelation greatly angered Nefarious, and again triggered his malfunction, causing him to pick up more radio signals of Lance and Janice. Lawrence had the robot troop in the room whack Nefarious over the head, and he went back to normal. Nefarious ordered Lawrence to kill them so they could not meddle in his plans. Proclaiming he would carry out his orders, Lawrence suggested Nefarious engage the safety on his gun so as not to kill any more troops. Nefarious shouted at Lawrence that the blaster was not even loaded, and tried to demonstrate this by aiming it off to the side and pulling the trigger. A shot did fire, bouncing off the walls of the room until it hit the frightened robot trooper.

Frustrated by killing another one, Nefarious went over to his desk and hit the red button to buzz the door open, shouting "Next!" to signal another trooper in. As the door opened, all of the shaking troops hesitated to enter, fearing they would end up like those auditioning before them. Through the rest of the Breegus System, Ratchet and Qwark continued their attempts to find Clank, and were eventually assisted by Azimuth, who wanted to rectify his mistakes and bring back the Lombaxes with Ratchet. In Axiom City, Ratchet discovered a large amount of Nefarious' hold on Polaris, and confronted Pollyx himself. Tossing aside the weak alien, Ratchet and Azimuth discovered the location of another Obsidian Eye, which they planned to use to get in touch with Clank. After, they received a transmission from Dr. Nefarious. He was glad to see Ratchet would witness his greatest triumph, and that he had met the "shame" of the entire Lombax race.

Ratchet asked if Nefarious was still up to his old plans, such as "Trying to turn everyone into robots", or "good old-fashioned galactic domination" and the doctor pondered whether he should allow Ratchet to find out or just kill him. As Nefarious ended the transmission, an alarm went off in the Pollyx Industries building, alerting that a large destructive machine was tearing through the city: the VX-99. Nefarious had sent it in the annihilate Ratchet and Azimuth, and it was destroying the area to ensure they did not escape. Ratchet did manage to defeat the monstrous machine, and continued to come after Clank. Back at the Nefarious Space Station, Lawrence again contacted the doctor via hologram. They were discussing the procedure to rewind time with clock. In order to reset everything according to Nefarious' needs, Lawrence said Pollyx had estimated that the procedure would take 183 paradoxes, and 184 should the Blarg participate. Since Dr. Nefarious wanted to make it so every hero would lose their battles in the past, it seemed he would enter into an alliance with the Blarg, among Ratchet's defeated enemies.

Lawrence advised that Pollyx's scientists examine the Orvus Chamber before testing the clock. Nefarious then leaped in front of Lawrence's holographic image and said "What's the matter, Lawrence? Chicken?" He then imitated a chicken to mock his butler, and at that moment, Lord Vorselon teleported into the room and loudly announced the doctor's name. The sudden announcement behind him caused Nefarious to let out a startled scream and jump high into the air. As he fell back down, Lawrence pretended to try and catch him, only for him to fall right through the hologram and hit the floor. Lawrence then sarcastically apologized as his superior picked himself up, and Nefarious simply scowled at him. Going back to his desk, Nefarious listened as Vorselon gave his report. He had discovered that the two Lombaxes had destroyed the VX-99, and he was tracking them. Nefarious angrily proclaimed "Unacceptable! I practically handed those squishies to you on a silver platter. How could you be so utterly incompetent?!".

Dr. Nefarious threw a small glass globe sitting on his desk at Vorselon in anger, but Vorselon avoided it by teleporting out of its way, leaving it to shatter against the wall, and then reappearing behind Lawrence's hologram, shivering with fear at Nefarious' rage. As Lawrence left them alone, the doctor reminded Vorselon that if the Lombaxes found the clock, their plans would be ruined, and his body would never be recovered. Nefarious declared he would bring in "specialists", and pressed the button to buzz his office's door open. Three large female robots walked in: Cassiopeia, Carina and Libra, leaders of the Valkyrie mercenaries. Nefarious had requested an audience with them at his station. The doctor introduced them individually, referring to Libra with distaste compared to Carine and Cassy due to her masculine voice and behaviour. Nefarious reminded them of how their original colony had been lost decades ago in the tragic Erebus supernova. He requested their services in exchange for returning their lost colony.

The Valkyries accepted, and along with Vorselon, fought against Ratchet and his allies while Nefarious got closer to accomplishing his goal. Eventually, Ratchet managed to contact Clank, and Clank told him to confront Nefarious in the past on Zanifar so that he could save Orvus. Using a time portal projected by Sigmund, Ratchet went through a series of events both in the present and past Zanifar, and eventually got inside the Tombli Outpost in the past, right when Nefarious was interrogating and torturing Orvus. After Orvus vanished and Clank's image appeared, Ratchet exclaimed in confusion, alerting Nefarious to Ratchet's presence. However, Ratchet had taken out a Constructo Bomb Glove grenade, and threw it at Nefarious before fleeing. The bomb exploded inches away from the doctor's face, and as he yelled in agony, it was shown in slow motion that he was knocked back. His right eye was damaged, a crack forming up the side of his green dome, his red pupil knocking loose, and giving Nefarious a permanent scar.

The Doctor angrily ordered his troops to annihilate Ratchet, but the Lombax escaped back to the present. Back at the Nefarious Space Station, in the present, he was sitting on his coach with Cassiopeia, laughing while he told her of how he mocked Clank as a prisoner. Cassy grew closer to the Doctor, saying "Dr. Nefarious, you have such a wonderful sense of humor, and you're so, so..." However, Nefarious suddenly realized what Ratchet had done. The bomb scarring his eye in the past took effect in the present, and Nefarious said "Uh oh..." as the scar formed and his eye fell limp. He then angrily screamed Ratchet's name. Much later, Ratchet fought Vorselon in combat, for the second time, and Vorselon revealed his new suit had been upgraded by Nefarious. He was still defeated, once again escaping, head intact, returning to the Doctor's station. In Nefarious' office, the two played against each other in a holo-vid game with Dr. Nefarious fighting Captain Qwark.

Lord Vorselon's Qwark character was at a disadvantage because Vorselon had no arms. Defeating him, Nefarious loudly gloated in Vorselon's face and sat back down. Lawrence then appeared in a hologram and reported that he had captured Clank and the Orvus Chamber, as Clank had unknowingly led them right into it just as Nefarious predicted. Pleased with this news, Nefarious told Lawrence to notify the Valkyries, and mobilized the next phase of his plans: Unnecessarily Evil Initiative Omega-91. Lawrence went to inform the Valkyries of the next step in their plot, and Nefarious' door bell rang the next moment. A light voice said that it was time for Nefarious' massage, but the annoyed Doctor pointed out he did not send for a massage. He told the person at the door to go away, but the voice briefly got deeper and again asked him to open the door. When it opened, a female nurse appeared, and Nefarious' loose eye fell limp again. It was Qwark in another poor disguise, and the Doctor recognized him, but played along with his ruse, making the Captain believe he was fooled.

When the Lombax hero and elder antihero arrived, Nefarious was complaining with Cassiopeia about trying to kill Ratchet as per Unnecessarily Evil Initiative Omega-91's procedure. Ratchet later successfully defeated and killed Cassiopeia on Vapedia and rescued Clank, the Valkyries finally beaten completely, although Lawrence did not know what happened on Vapedia. The reunited duo left the Valkyrie Citadel and headed toward the Nefarious Space Station, where the disguised Qwark aided them in getting inside their enemy's stronghold. Alister wanted to misuse the Great Clock to change history and bring back the Lombaxes, leaving the team when Ratchet and Clank refused to let this happen. Clank managed to sneak in an air duct and came to a vent above Nefarious' office. There, Nefarious told his computer to take his dictation: "Things to do once the clock is under my control. Number 1: Double-cross remaining Valkyries and retire Lord Vorselon. Number 2: Reestablish vendetta against organic life forms! And number 3: Iron socks." This revealed that Nefarious intended not to keep the deals he made as his subordinates had failed him for too long. Clank successfully scanned the Doctor after he was done recording his to-do list. This allowed Ratchet to apply a holo-guise of the doctor and freely explore the station undetected. Despite this, Ratchet's height did not change, but Nefarious' minions still fell for the trick.

Getting updates in Dr. Nefarious' plot from Lawrence, the disguised Ratchet wanted him to order Nefarious' fleet to land at the station. This could not be done until Ratchet destroyed the nearby asteroids blocking the landing bay with the station's Hypernova Defense Laser with help from Pollyx who he sent to the brig Ratchet made sure all the vessels that he could contact landed. After all the ships landed, Ratchet used the laser to destroy every ship as well, giving Nefarious no escape from his station. As Ratchet and Qwark made their escape, they were confronted at the bottom of an elevator by the real Nefarious, flanked by two guards. Qwark, still believing his facade was working, quickly said "You're not Dr. Nefarious!" to Ratchet and slapped him, accidentally deactivating his holo-guise. Ratchet told Nefarious that he could not use the clock, as nothing he could want was worth risking the entire universe. Nefarious said that there was, and he had his three greatest enemies to thank for it. He then had several flashbacks that showed everything he had been through since his first defeat at the hands of Ratchet and Clank, after which the Doctor explained his ultimate goal to the trio.

"With the clock under my control, I'll be able to wrong all the rights in the universe. Every villain who has ever stumbled will get a do-over! Every protagonist's triumph will be reversed! Until, finally, a new present is created... in which the heroes always LOSE!!! Hahahaha!"

- Dr. Nefarious' plan to remake history with the Great Clock

After capturing them after a futile escape attempt by Qwark, he attached Ratchet and Clank to an asteroid, prepared to launch from his Asteroid Flinger 5000, which he installed in case he ever needed a "super ironic death scenario." Ratchet said that the Doctor was making a mistake, and Nefarious said "Time will tell." Bidding farewell to his old nemeses, Nefarious laughed evilly as he prepared to press the launch button on the machine. However, while laughing, the Doctor again froze and picked up Lance and Janice signals. After an awkward pause, a nervous trooper standing by Nefarious took his hand and pressed the button. Ratchet and Clank were flung far away to Morklon, but eventually returned to the station. Lawrence had come from the clock in another ship, and the Doctor was preparing to return to the facility to finally complete his plans. He was distraught by the duo's return, thinking they were supposed to be dead, unaware that the Zoni had helped them in the crash.

Ratchet and Clank told Dr. Nefarious to shut down his transport and surrender on behalf of galactic authorities. He approached the duo and mocked Clank for "running right back to playing backpack to a squishy" rather than fulfilling his destiny. He told Clank "You're nothing but a pathetic sidekick," prompting Lawrence to sarcastically say "We should hang out some time" to Clank. Ratchet, angered by his mocking of Clank, stood up to the mad doctor, they then prepared to defeat Nefarious once and for all, and the Doctor rose into the air with booster jets in his feet and extending his wings, saying that he would rewind time after killing the two so he could do it over and over again. Before attacking Ratchet & Clank, Nefarious ordered Lawrence to fall back to the outer perimeter, allowing no damage to befall their ship. A fierce battle immediately ensued, going around the ring of the platform near the station, which was eventually destroyed by the Hypernova Defense Laser after the Doctor ordered Lawrence to activate it. The battle then went onto Nefarious' ship as it flew away from the station, setting course for the clock.

Damage to the ship during the fight caused it to speed into an inevitable collision with the Nefarious Space Station, and Lawrence had no control over the auto-pilot. Despite getting assistance from his butler, Nefarious was defeated a second time, and fell screaming to his ship's surface. He then got up and began malfunctioning more than ever before due to the damage he sustained. He fell on his back with his mouth wide open as his brain picked up signals of opera music. He then sprang up as a lottery sound played, and fell forward. As the ship came closer to crashing into the station, Ratchet grabbed Nefarious and urged him to tell how to disengage the auto-pilot. The doctor would not respond, and his eyes continued to spin in circles while eccentric laughter was heard in his brain's signal. Ratchet smacked Nefarious to try and snap him out of it, but this merely caused the doctor to get up and dance to a yodeling tune in his brain. Nefarious then collapsed completely, his eyes popping out and the signals in his brain dying away.

Lawrence then took the escape pod, leaving Ratchet, Clank and the crumpled body of Dr. Nefarious on the ship. However, General Azimuth appeared and saved Ratchet and Clank before it collided as they jumped off the saucer and into his ship. Unbeknownst to anyone at the moment, Lawrence teleported the Doctor's unconscious body away. After the ship crashed into the dome of the station, it's head was given a scar and broken eye just like the original Nefarious. It then completely exploded, and the Doctor's villainous plot was finally ended.

During the credits, radio announcers Kip Darling and Pepper Fairbanks reported that the remains of neither Dr. Nefarious nor Lawrence were found anywhere in the station's rubble and that Polaris Defense Initiative 1887-Upsilon was mobilized to locate them; galactic authorities proceeded with a manhunt to find the missing Doctor and his partner, making the arrest of them their highest priority.

Light-Eating Z'Grute rampage
"Well, HELLO, Mr. President! So kind of you to accept my invitation!" "Dr. Nefarious. I was wondering when you'd be showing up. Is that your new space station? Looks a little smaller than the last one." "Oh, you're hysterical! Let's see you crack jokes from inside the digestive tract ''of a Z'Grute!"

- Nefarious, declaring his revenge, and Ratchet Nefarious appears again as the main antagonist at the very beginning and one of the four protagonists during All 4 One At this point, the evil doctor and his butler's threat level had increased to from unknown to "alive and at large". With all the commotion, Galactic President Qwark acted on the situation, convinced that there was no danger, and assured the galaxy that everything was under control. Being interviewed by news reporters Kip Darling and Pepper Fairbanks via satellite, Ratchet and Clank gave their personal outlook on the predicament. They claimed they were retired and had full confidence that Qwark would be able to track down the enemy.

Meanwhile, in the depths of Planet Igliak, the doctor's new plan was already in motion. Dr. Nefarious set up a false award ceremony for the Galactic President, claiming Qwark was the world's greatest Intergalactic "tool" and that he would receive an Intergalactic Tool of Justice Award for defeating a Light-Eating Z'Grute in the past, which never occurred. Ratchet and Clank, suspicious of the award, went along with Qwark in receiving it. Out from behind, Dr. Nefarious and Lawrence on a miniature hovercraft appeared and the menacing doctor revealed his plan to the heroes, that which he would unleash the Light-Eating Z'Grute upon the city to kill them. However, in an unexpected turn of events, the Z'Grute raged uncontrollably, giving Nefarious no control over the creature. Reaching for Lawrence for help, Lawrence cowardly walked away, stating it was time for him to tender his resignation, leaving Nefarious forced to join forces with Ratchet, Clank and Galactic President Qwark to prevent the Z'Grute from causing more damage through the city of Luminopolis.

The rare creature attracted the attention of a vast and powerful machine known as Ephemeris the Creature Collector. The heroes were accidentally transported to a marooned planet called Magnus by the machine, a planet containing a dark secret that not even its caretakers fully understand, and are forced to work together for their own survival in finding a way off the unknown planet. The foursome awake in a testing hub in an unknown location and are forced to participate in testing to disguise themselves as minions. The four soon encounter a little girl named Susie, who assists them in escaping the facility.

Trapped
After escaping the creature collecting facility, the foursome encounter Cronk and Zephyr who report via hologram to inform them that they were traveling to Magnus to retrieve them but got stuck in an asteroid field and until they are assisted, there was no way for them to get them. Realizing they were trapped for good, the four gazed, stunned by the environment they were transported to. Susie then proceeded to direct the foursome to a small village inhabited by a race of creatures known as Tharpods, the natives of the planet. One of them informed the four of the background behind Ephemeris, claiming it to have been around for over a hundred years, snatching the universes' most dangerous creatures and transporting them to their planet. The native referred them to the Creature Collector's emissary, Commander Spog, who had been attacking the Tharpods and protecting the machine for years. The Tharpod figured Ratchet and Clank for candidates to help protect the planet from the chaos caused by Ephemeris and Spog, but Ratchet, retired from heroics, was unenthusiastic about going on another adventure to help, but confirmed he would notify the Polaris Defense Force to assist them once he was off the planet. Ratchet had a change of heart, however, when he heard Susie's parents were killed during Ephemeris' raid on Totem Fi, she was an orphan, and agreed to help track down Commander Spog.

After destroying a wigwump while using jetpacks on their trail to Spog, Clank came across a holo-journal narrated by Frumpus Croid explaining the attack of Uzo City orchestrated by Spog and his armies and that the controller of Ephemeris had a plan for the creatures the machine had been capturing all those years. Nefarious jokingly commented that he wasn't going to carry the exhausted Qwark if he passed out and the pair continued their search for Spog.

The pair eventually tracked down Spog and after a long chase after him, defeated Spog. Spog was near-destruction, but agreed that if Nefarious repaired the damaged they had caused him, he would, in return, tell them how to defeat Ephemeris. Once Spog was repaired, the commander told them that only the architect who lived in the forest of the blue rocks had the answers they were looking for. Qwark commended Nefarious' good actions, saying that he did the right thing, to which Nefarious countered angrily "Get bent".

Return of the Loki
During the adventure, Nefarious constantly complained about Qwark and even tried to kill him at one point, though because Qwark moved Nefarious accidentally fell off the edge and was saved by Qwark, this filled Nefarious with uprise and gave him a change of heart.

Towards the end of the adventure, Nefarious started treating the others as if they were friends, and during the final battle against the Loki Master, Nefarious saved Qwark and dealt the finishing blow to the Loki.

After Cronk and Zephyr landed, Nefarious and Lawrence escaped in their ship, but during the end credits Nefarious was seen looking at a picture of him with Ratchet, Clank and Qwark with a sad look on his face, as he was sad to leave his friends.

Just like old times...
Nefarious met Clank on a planet and they began insulting each other after watching the events of Up Your Arsenal. Nefarious claimed that he should have killed Ratchet and Clank when he had the chance.

Galactic Idol
According to the IRIS Supercomputer, Dr. Nefarious entered Galactic Idol with a song titled Crushin' on Squishies. He was eliminated on the first round and the single sold one copy which was used to torture prisoners on Ebaro. However, before Ratchet battled with Giant Klunk in Metropolis in Ratchet and Clank: Up your Arsenal, Lawrence accidentally activated a hologram recording of what could be Nefarious' original entry, which was a song including the lyrics ''You Are My Robot Lover. ''It may be the same song however.

Personality
Doctor Nefarious was characterized as being extremely evil, eccentric, maniacal and insane. He had absolutely no remorse in his actions and cared only for his personal gain. He showed enjoyment in his diabolical endeavors. His treatment of the Fongoids also showed much cruelty, and his disregard for Courtney Gears' affections showed him to be very cold and uncaring, despite Qwark's insulting her offending him later, suggesting he retained at least some feelings for her but chose not to show them. He showed complete impatience for his servants failing him, shown when he threw a complete fit of rage at Lord Vorselon and entirely double-crossed the Valkyries possibly due to Cassiopeia's disobedience. The Doctor was also well known for being conceited and egomaniacal; his inventions and structures were usually made in his image, his robot servants commonly resembled his features and/or had mannerisms like his, and he tended to pass his ideals onto his subordinates.

However, the final cutscene after the credits of All 4 One implies that his companionship with the heroes may have changed him, as he is shown close to tears while looking at a photograph of him, Ratchet, Clank and Qwark.

Despite the Doctor's extreme hatred for organic life. He was not above working with them to obtain his desires. Nefarious has also shown to be extremely cunning, knowing full well how to manipulate others to get what he wants. This is shown by how he forged an alliance with the Tyhrranoids, the Fongoids, and the Zoni; as well as how he had Lord Vorselon and the Valkyries come to his side with the respective promises of a new body and a home planet. However, that did not stop him from betraying them when either their usefulness had run its course or they disappointed him.

Despite the doctor's self-proclaimed genius (which was undeniable, as masterful engineering must have been required to build weapons as advanced as the Biobliterator or the Hypernova Defense Laser), his common sense at times was questionable by his actions. Two prominent examples of this are his failure to recognize Lawrence's sarcastic responses towards him, and his rehearsal of "Night of the Living Squishies" play with a loaded gun without engaging the safety because he initially believed it was not loaded.

Short circuit freezing
"You really should have that looked at..."

- Lawrence on Dr. Nefarious' glitch Dr. Nefarious often had a tenancy to short circuit and freeze in times of extreme stress or excitement. The first visible sign of Nefarious freezing was the gears in his brain speeding up in movement. When he did completely short circuit, his entire face and body would freeze in place. Simultaneously, his brain would pick up radio signals, particularly of the soap opera, Lance and Janice. His cranial gears would be stuck, unable to turn while slightly twitching, as smoke and sparks also came out of his brain. Each time this happened, he was whacked on the head by an underling, often Lawrence, to unfreeze him. Completely unaware of this problem, he would continue what he was doing as if nothing happened afterwards.

According to Lawrence, whacking Dr. Nefarious was always the best part of his day; however, he was shown to often get annoyed by the repetitive situation in addition to minor amusement. His first crash was shown at the end of Deja Q All Over Again, and the problem continued throughout the course of his campaign in Solana. His freezing continued while stranded on an asteroid and later while on the Great Clock. Eventually, after sustaining significant damage, his short circuiting caused his body to randomly move about, acting out the varying radio sounds he picked up, before finally collapsing.

Abilities
"When I'm finished killing you I think I'll rewind time. So I can do it again. And again. AND AGAIN!!!"

- Dr. Nefarious before battling Ratchet and Clank

After being turned into a robot, Dr. Nefarious acquired a vast array of powers and abilities that greatly contributed to his fighting skills. His hands were made into sharp metal claws for close-quarters combat. He could also fly with booster jets in his feet. A pair of retractable wings extended from his back and were used to keep balance when flying, also allowing him to hover low above the ground. Nefarious also showed limited agility, able to perform flips in the air. The doctor also wielded blasters on occasion, such as duel ones that fired red-purple laser beams. Mainly, Nefarious controlled and fired various forms of energy from his hands, utilizing many different kinds of attacks against his enemies as demonstrated numerous times in his battles with Ratchet and Captain Qwark.

Dr. Nefarious could rain down rainbow-like streams to hit targeted areas, raise walls of energy from the ground, and move a floating circular vortex. He could also project holograms of himself that would charge and slash with a claw and lob purple energy balls that created shockwaves when hitting the ground. While flying, he could project a blue dome shield, fire continuous purple or orange energy beams, conjure a barrage of missiles that would target all over the ground, and send rod-shaped streams of energy across the ground. Some attacks exhausted the doctor and took much power; after some attacks, he would stumble backwards and hold his head briefly before standing himself upright, and when initiating others, he let out a loud shout.

Dr. Nefarious would also occasionally summon his robotic minions to aid him in battle, having them teleport onto the battlefield, or simply order assistance from Lawrence, who used the doctor's separate weapons to help him. It was not often that Nefarious battled his adversaries himself, often having his servants do his work for him unless all options were exhausted or he had a personal desire to fight.

PlayStation All-Stars Battle Royale
Nefarious appears in San Francisco where his Nefarious Space Station is located, after some time he will move the players onto the station and begin attacking them with help from the Hypersonic Brainwave Scrambler. In this game he is allied with the Chimera, a species from Insomniac Games' Resistance series.

Nefarious also appears as a Minion that is unlocked by reaching Level 80 with 3 characters.

Nefarious (along with the Helghan army from KILLZONE and Zeus from God of War) was originally going to be the final boss of PlayStation All-Stars Battle Royale, but was scrapped for Polygon Man.

Trivia

 * Doctor Nefarious is considered the main antagonist of the series, mostly due to his status as the archnemesis of Ratchet, Clank and Captain Qwark. He also has had more appearances and mentions than any other villain in the franchise; he is the only one to have a speaking part in five games and at least a mention in every game since his introduction. Insomniac Games consider him an adversary that Ratchet and Clank will never seem to be able to kill.
 * Armin Shimerman, the voice of Nefarious, played a character named Quark in Star Trek: Deep Space Nine.
 * He had a screechy laugh & was also one of the few Ratchet & Clank villains who didn't die. Another is Otto Destruct, villain in Size Matters & another is possibly Qwark for being main antagonist of Going Commando.
 * It's possible that he was once a member of Stuart Zurgo's unnamed spieces due to the ears & similar head shape.
 * According to Qwark, it is possible that Nefarious wasn't a real doctor and the title was only self-proclaimed.
 * During Secret Agent Clank,  Klunk made a clone of Nefarious which had his abilities (and possibly memories) and was programmed to obey Klunk, he was destroyed by Clank in the final battle against Klunk.
 * Nefarious used the term "annihilate" extremely frequently when he wanted something or someone destroyed, making it one of his main phrases. Being conceited, Nefarious passed this among other traits onto his Nefarious troopers.
 * Nefarious' habit of calling organic life forms "squishies" was also passed onto all of his followers, save Lawrence, the Valkyries and the Terachnoids; Klunk, even the Tyhrranoids and Vorselon used the term, despite being organic at one point (both were made robotic and into a cyborg, respectively).
 * As depicted in concept art, Nefarious was originally supposed to have a cape before his wings were added.
 * Nefarious appeared in the Dreamtime level as a memoir in Size Matters.
 * Nefarious' broadcast to all of Solana's robot citizens appeared on some of the monitors of the IRIS Supercomputer.
 * Throughout A Crack in Time, several references were made about Nefarious' relationship with Cassiopeia. During his boss battle, it is possible to hear him say "That one's for Cassiopeia!" Also, on a space radio station, it can be heard that he requested a song for her, sending the message through the D.J. "I never thought I'd love again, 'til I met you." The D.J. then said "Well, it looks like this doctor's specialty is love."
 * It is unclear why Nefarious was going to betray the remaining Valkyries if he loved Cassiopeia and they were fellow robots. It is possible that this was merely out of spite since she failed to stop Ratchet, or he may have been planning to betray her anyway out of selfishness over having possession of time itself.
 * Nefarious' armor plating seemed to change at certain points. Mainly, it was red, but it sometimes appeared to be orange or dark yellow. Also, in his first appearance up to the ending of Quest for Booty, Nefarious's face was the same color as the rest of his body (blue), and his eyes appeared to be digital. In A Crack in Time, Nefarious's eyes are now black with red digital pupils, and the "glowing" parts of his arms and legs are red.
 * Nefarious is an unlockable skin for Ratchet in both Up Your Arsenal (multiplayer only) and A Crack in Time.
 * Ironically, the blaster Nefarious' Future series action figure comes with is very similar to the blaster Qwark was first seen using in Ratchet & Clank, in an advertisement for Al's Roboshack and the training course in Qwark's headquarters. Even more ironically, the blaster that Nefarious was using for Night of the Living Squishies was the same as the one Qwark used in A Crack in Time, only green instead of orange. It even had the captain's Q-shaped symbol on the handle.
 * Nefarious' mother, at one point, suggested he was a disappointment.
 * In A Crack in Time, it is interesting to note that the Chimpositron actually worked on Nefarious during the final stage of his boss battle; it could turn him into a monkey when Ratchet battled him on top of his space ship. It worked no matter how much health he had, and counted as defeating him (as the cutscene followed after). It was best to throw out a Groovitron first so he couldn't hit Ratchet, as it took a while for it to work on him.Nefarious symbol.png
 * Nefarious' birthday is on the 9th of March as shown in the Ratchet & Clank Future 2010 Calendar.
 * According to the trailer for All 4 One, Dr. Nefarious's armor plating has changed to violet instead of deep blue or black.
 * Nefarious is a big fan of the holo-vid series Secret Agent Clank, and in Up Your Arsenal, he usually referred to Clank as Agent Clank.
 * Nefarious is a large enemy in the PlayStation Home Firing Range (future).
 * The Loki Master also states that he is a fan of Nefarious' work.
 * Nefarious' home planet could be considered Kerwan as he went to school there with Qwark in ninth grade.
 * It is also possible that his home planet is Rilgar, seeing as how that was where he set up his base when he first became a villain.
 * Dr. Nefarious is perhaps one of the only two main antagonists to battle Ratchet and Clank without assistance, the other being Captain Darkwater. Nefarious, instead of battling them in a giant mechanical robot or gain special powers, battles them with his own abilities.
 * Nefarious is the only Ratchet & Clank villain to be an antagonist in more than two games, being the main antagonist in Up Your Arsenal and A Crack in Time, and being a secondary antagonist in All 4 One.
 * It is possible that Nefarious' color was changed to purple in All 4 One because Clank's color had to change to blue since Qwark was green.
 * His eye was broken and very loose in A Crack in Time after Ratchet threw a bomb at his face, but in All 4 One he seemed to have control over it like it never broke. Considering how his eye fell out of his socket at the end of A Crack in Time, he might have replaced it with a functional one, though some fans say otherwise as they see his right eye fall out and not his left. Insomniac Games has not officially said this, but both eyes may have fallen out and Lawrence replaced both.
 * Nefarious's original blue-black suit is an unlockable costume in All 4 One. This costume also repairs his cracked head.
 * Dr.Nefarious first name claimed to be Miles and planet Mylon was named after himself.
 * Nefarious said he hated biology at school, however he excelled in this domain since he created the amoeboids.

Appearances

 * Ratchet & Clank: Up Your Arsenal
 * Ratchet: Deadlocked
 * Ratchet & Clank: Size Matters
 * Secret Agent Clank
 * Ratchet & Clank Future: Tools of Destruction
 * Ratchet & Clank Future: Quest for Booty 
 * Ratchet & Clank Future: A Crack in Time
 * Ratchet & Clank: Issue 1: Ears of War
 * Ratchet & Clank: Issue 2: Friends with Benefits
 * Ratchet & Clank: Issue 3: Lost and Spaced
 * Ratchet & Clank: Issue 6: Bros Before Foes
 * 8-Bit Mini Mayhem
 * Ratchet & Clank: All 4 One
 * Ratchet & Clank: Full Frontal Assault

Non-canon

 * PlayStation All-Stars Battle Royale
 * PlayStation Home
 * Copernicus Qwark's Awsomely Epic 3D Adventure Through Time & Space
 * Ratchet & Clank 10th Anniversary Limited-Edition Poster Series

YouTube videos

 * Nefarious introduction.
 * Nefarious vid-comic boss battle.
 * Nefarious ACIT boss battle.