Nefarious

"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!"

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

Doctor Nefarious was a robotic mad scientist who hated organic life forms, despite formerly being one himself. He was also the archenemy of renowned intergalactic 'superhero,' Captain Qwark, and later a recurring nemesis of the courageous duo, Ratchet and Clank. Nefarious was the primary antagonist of Ratchet & Clank: Up Your Arsenal, plotting to turn all organisms into robots. He was eventually defeated, but survived. He made several cameos in further games, recurring more than any other villain in the series, and returned as the primary antagonist in Ratchet & Clank Future: A Crack in Time. At this point, he planned to gain control of time itself and remake history, but was again defeated.

Early life
"I always hated Biology!"

- Dr. Nefarious

In high school, Dr. Nefarious attended the same 9th grade Biology class with Copernicus Qwark. He had been constantly bullied and humiliated at the hands of Qwark, who was twenty-six years old and three times Nefarious' size 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." 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 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
"This isn't over, Qwark! I swear, I will return some day to destroy you, and bring Metropolis to it's knees!" "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 (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 freeze up.

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." Due to Lawrence's lazy job and Nefarious being unaware of the glitch in the first place, the repairs never happened.

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! Mua-ha-ha-ha-ha-ha-ha-ha-ha-ha-ha-ha-ha! 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 name "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 onboard, 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 after he arrived 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. 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 frustratedly said "Fine. I'll do it myself."

Showdown with Ratchet
Dr. Nefarious faced off against Ratchet 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, Ratchet 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 fell 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 right away, having been preoccupied with guitar practice. The doctor ordered his butler to "Begin the transformation!" and shouted at him when he continued to be distracted by his guitar. At the press of the activation device, the second Biobliterator changed into an immense, powerful mechanoid. Laughing maniacally, Nefarious prepared to use his monstrosity to bring about the Age of Robots as he and Lawrence teleported to the cockpit. 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. Distraught at this, Nefarious yelled in frustration and disbelief "No! I don't believe it!", and Qwark replied with "Believe it, toasterhead!"

Ratchet and Qwark managed to defeat Nefarious in the air and destroyed the 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 Dr. 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 far 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 BORING!"

- Dr. Nefarious to Ratchet and Clank

Dr. Nefarious and Lawrence were stuck 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.

Much later, after Ratchet and Clank competed in DreadZone and saved the contestants and fans from the evil Gleeman Vox, Dr. Nefarious and Lawrence came near the DreadZone Station, where they had hoped to land. Before they could reach the station, it was destroyed by Vox's self-destruct. Nefarious asked Lawrence what was going on, as he had said they were coming within range of a space station. Lawrence said he had no idea it would suddenly explode, prompting Nefarious to angrily scream, freezing up and triggering the soap opera signal in his brain again. The two were still forced to aimlessly float through space; however, after some time (though not as long as Lawrence calculated), the asteroid drifted to the Breegus System in the Polaris Galaxy.

The rock picked up speed and turned into a ball a fire after drifting to planet Zanifar. It crashed in the Tobalia village of a local Fongoid tribe, forming a crater, which was barricaded. Dr. Nefarious and Lawrence sought refuge with the tribe, arriving as they were in the middle of celebrating spring break.

Arrival in Polaris
"How could I have been defeated by the likes of you? Why had the universe been tipped in your favor?"

- Dr. Nefarious to Ratchet and Clank

While living with the Fongoids on Zanifar, Dr. Nefarious tried to find out 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, which maintained time and space so that the cosmos would never be threatened or damaged. 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 put his organic life form vendetta on hold, again working with "squishies" if it benefited 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 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?"

- 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 hear 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 the Cragmite Empire and Emperor Tachyon, 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 to being a hero after taking some time to do film making, Talwyn stayed behind, warning Ratchet that the system 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
"Shall I prepare the mnemonic station again?" "No. I've got a better idea." "But, sir..." "Patience, Lawrence. We have all the time in the universe..."

- Lawrence and Dr. Nefarious, having recaptured Clank

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 conrol 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 henchman 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 unconcious 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 subconcious. 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 was nearing Sigmund's location, and Lawrence was closer to finding him, 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 veangence, and said "They say I'm egomanical". 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 vorselons 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, 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 monsterous 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 popping up of Vorselon right 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, and Nefarious starred angrily 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 deemed this turn of events unacceptable. saying "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 scar.

Dr. Nefarious angrily ordered his troops to annihilate Ratchet, but the Lombax escaped back to the present. Back at the Nefarious Space Station, in the present, Nefarious 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 was all of a sudden made aware of what Ratchet had done. The bomb scarring his eye in the past took affect in the present, and Nefarious said "Uh oh..." as the scar formed and his eye fell limp. He then angrily shouted Ratchet's name. Much later, Ratchet fought Vorselon in combat, for the second time, and Vorselon revealed his new suit had been upgraded with a new energy ball attack 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 the next phase of his plans would take shape: "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 doctor said he did not send for a massage. He told the person at the door to go away, but the voice briefly got deeper and said that he should just 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.

When the Lombax hero and elder antihero arrived, Nefarious was complaining with Cassiopeia about trying to kill Ratchet. 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 was confused what the Great Clock's use left the team. Clank managed to sneak in an air duct and came to a vent above Dr. Nefarious' office. There, Nefarious told his computer to record 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 never intended to keep his deals with most of his partners and now that Cassiopeia was killed he had no reason to help the remaining Valkyries. 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, acidentaly deactivating his Hologuise. Ratchet told Nefarious that he could not use the clock, as nothing he could want was worth risking the very universe's existence. 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.

The doctor explained his ultimate goal to the trio, and captured 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 referred to Clank as a pathetic sidekick, prompting Lawrence to sarcastically say "We should hang out some time." Ratchet, angered by his mocking of Clank, then prepared to defeat Nefarious once and for all, and the doctor rose into the air with booster jets in his feet, saying that he would rewind time after killing Ratchet so he could do it over and over again. Before attacking Ratchet, 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 around 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 yodoling 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 Nefarious on the ship as it was about to hit the station. General Azimuth, however, then appeared to save Ratchet and Clank before it collied, however, just before the ship crashed, Nefarious' body was not seen on it's surface. After the ship crashed into the station, The station's head was given a scar and broken eye just like the original Dr. Nefarious. It then completely exploded, and Nefarious' villainous plot was finally ended. During the game's credits, radio announcers Kip Darling and Pepper Fairbanks reported that Nefarious and Lawrence were not found after the station exploded, and that the Polaris Defense Initiative was mobilized, leaving his ultimate fate ambiguous.

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 a pair of booster jets in his feet. A pair retractable wings extended from his back and were used to keep balance when he flying, also allowing him to hover low above the ground. 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 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 his energy across the ground. Some attacks exhausted the doctor and took much power, as after certain ones 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 assisstance from Lawrence, who used the doctor's separate weapons to help him; it was not often that Nefarious battle his aversaries himself, often having his servants do his work for him unless all options were exhausted or he had a personal desire to fight.

Overload
"You really should have that looked at..."

- Lawrence on Nefarious' glitch

Dr. Nefarious often had the strange habit of overloading in times of extreme stress or excitement. The first visible sign of Nefarious overloading was the gears in his brain speeding up in movement. When he did completely overload, he would freeze, and simultaneously pick up radio signals, particularly the soap opera, Lance and Janice, via his head. His brain gears would also stop turning and be stuck. Each time this happened, he was whacked on the head by an underling, particularly Lawrence, to send him back to normal. According to Lawrence, whacking Dr. Nefarious was always the best part of his day. His first crash was shown at the end of The Shaming of the Q, and he did it numerous times through the course of his campaign in Solana. His freezing continued during Ratchet's search for Clank, until finally, after sustaining significant damage, his overloading caused his body to randomly move about, acting out the varrying radio sounds he picked up. Dr. Nefarious eventually collapsed, and his brain's radio signals faded away. It is unknown if Nefarious was aware of this problem.

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 on Metropolis, Nefarious accidentally activated a hologram recording of his original entry, which was a song called You Are My Robot Lover.

Trivia

 * Armin Shimerman, the voice of Nefarious, played a character named Quark in Star Trek: Deep Space Nine and voiced Andrew Ryan In Bioshock, the former of which Qwark was partially based on.
 * Since Lawrence escaped at the last moment in an escape pod, this may indicate that he retrieved Nefarious first, which is why authorities could not find him in his station's rubble. It is also interesting to note that Nefarious' body was not seen on the ship right before it crashed into the station, suggesting he slid off or was teleported away. Regardless of this possibility, the doctor's ultimate fate remains unknown.
 * Nefarious used the term "annihilate" extremely frequently throughout Up Your Arsenal and A Crack in Time when he wanted something or someone destroyed. Being conceited, Nefarious passed this among other traits onto his Nefarious troopers.
 * Nefarious' habit of calling organic life forms "squishies" was passed also passed onto the Nefarious troopers, as well as Klunk; he had apparently programmed both to follow his prejudice ideals, or was at least strictly enforcing organism hatred among his followers.
 * 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.
 * Klunk created a copy of Nefarious, the Robo-Nefarious suit, which he piloted during the final boss fight of Secret Agent Clank. This doppelganger had abilities based on the real doctor's powers. Klunk said that ordering Nefarious around from time to time was "therapeutic" and "fun," suggesting Klunk had a certain dislike for his creator.
 * In Tools of Destruction, when in the arena of planet Mukow, Captain Qwark could be heard over the loud speaker saying: "Will a 'Dr. Nefarious' please report to the concession stand; we recovered your wallet."
 * On the Ublik Passage,a group of Space Pirates could be heard saying "I saw him ridin' on one of them asteroids in the Corvus Nebula, a brain like clockwork and such, he also had a round fella with him, he called him 'Janice'" most likely referencing Nefarious.
 * Nefarious also appeared on some of the monitors around the IRIS Supercomputer.
 * Throughout A Crack in Time, it was referenced several times that Nefarious had become Cassiopeia's "boyfriend." During his boss battle, it is possible to hear him say "That one's for Cassiopeia!" among other sayings if he hits Ratchet. 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 he 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 is the only villain to have appeared with at least one speaking part in four games, and has also had at least a cameo in every game since his introduction and before his return, making him the most recurring villain in the series' history. This has made fans consider him the primary antagonist of the entire series, a belief backed up by his longtime rivalry with Captain Qwark and him being the biggest threat so far in trying to take over the Great Clock. Others believe that Emperor Tachyon held this position due to his connection and history with Ratchet. The true primary antagonist is debatable.
 * Nefarious' armor plating seemed to change at certain points. Mainly, it was red, but it sometimes appeared to be orange or dark yellow.
 * Nefarious is an unlockable skin for Ratchet in both Up Your Arsenal (multiplayer only) and A Crack in Time.
 * Ironically, the blaster Nefarious' action figure comes with is the same kind of blaster Qwark was first seen using in a commercial for Al's Roboshack, demonstrating malfunctioning weaponry. Even more ironically, the blaster that Nefarious was using for Night of the Living Squishies was the same kind as the one Qwark used as his main weapon in A Crack in Time, only green instead of orange. It even had the captain's Q-shaped symbol on the handle; the scene in the play where Nefarious had it may have been the doctor stealing his nemesis' weapon from him.
 * Despite being the main villain of two games, Nefarious was not the final boss in either one, but the second to last; in Up Your Arsenal, the final boss was the Biobliterator which he piloted after retreating from Ratchet, and in A Crack in Time, Azimuth was the final boss.
 * It is interesting to note that had Nefarious's plan succeeded and every hero's victory was undone, that his first defeat to Captain Qwark on Magmos would never happen and he therefore would still be an organic life form. In theory, this would have caused a time paradox, as if Nefarious still was an organic life form, it was possible that he didn't plan to turn squishies into robots, therefore the battle against him in the Bioblitorator and Ratchet & Clank hadn't occurred, he hadn't drift at Polaris with the asteroid and never had chance to use the Great Clock to make it so heroes always lose.
 * Nefarious' plan to destroy all organic life is similar to IG-88's plan to start the "droid revolution" to destroy all "organisms" in the Star Wars' expanded universe.
 * 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 him, and 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.
 * Despite Nefarious' hatred against organic lifeforms, he has been seen working with them in both games where he's an antagonist: In Up Your Arsenal, he is working with the Tyhrranoids, although he was probably planning on turning them into robot's, and in A Crack In Time he's working with Terachnoids.
 * Nefarious' birthday is on the 9th of March as shown in the Ratchet & Clank Future 2010 Calendar.
 * Nefarious' name could be a reference to an antagonist from the Crash Bandicoot, Dr. Nefarious Tropy, from befriended developer Naughty Dog, who also had an affection for time-manipulating devices.

Appearances

 * Ratchet & Clank: Up Your Arsenal
 * Ratchet: Deadlocked (cameo)
 * Ratchet & Clank: Size Matters (cameo)
 * Secret Agent Clank (doppelganger)
 * Ratchet & Clank Future: Tools of Destruction (cameo)
 * Ratchet & Clank Future: Quest for Booty 
 * Ratchet & Clank Future: A Crack in Time

YouTube videos

 * Nefarious introduction.
 * Nefarious vid-comic boss.
 * Nefarious UYA boss battle.
 * Nefarious UYA ending.
 * Nefarious Deadlocked cameo.
 * Nefarious QFB ending.
 * Nefarious ACIT boss battle.