|Trophy: Mutation Complete|
|Defeat the Mutant Protopet.|
Defeat the mutated Protopet is the final mission in Going Commando. After breaking into Megacorp Headquarters, Ratchet and Clank met Angela Cross, who caught up with them, only for Clank's admirer to reveal that disgraced hero Qwark had been planning the Protopet crisis to stage his comeback. At that point, Qwark revealed he had been impersonating Abercrombie Fizzwidget the entire time, and filmed a broadcast to be sent around the Bogon Galaxy framing Ratchet, Clank, and Angela as responsible, while he attempted to use Angela's gadget, the Helix-o-morph, to cure it. Instead, it mutated the Protopet into the Mutant Protopet, which then swallowed Qwark before storming off. It was then up to Ratchet and Clank to defeat the Mutant Protopet.
The Mutant Protopet's main attacks are curling up into a ball (surrounding itself with a shield) and rolling towards you to deal damage, and spitting out a large horde of Protopets, at which point it will watch them attack you until they are all gone. When it rolls towards you, it does so in a straight line, but will aim relatively late thus giving you little time to actually avoid it, after which it will repeat this for around three to four times. Periodically, ammo crates will appear, as well as Tractor Beam bombs, both of which it will try to swallow and spit at you to deal more explosive damage. The former will result in a swarm of small missiles, and the latter into large explosive rocks. The roll can be avoided by either using a boost jump or the Charge Boots, whereas the other tanks can be simply be dodged normally. As usual, the Shield Charger can be used to help absorb damage, but should not be relied on.
To attack the Protopet, wait until you are safe from its rolling attack, and then fire. Weapons such as the Bouncer, Hoverbomb Gun, and Minirocket Tube are particularly helpful, while other weapons should be saved for the other smaller enemies that appear. When a horde of Protopets appear, use the Plasma Coil to take them out (if upgraded to the Plasma Storm, this can be near instantaneous), or other area of effect weapons such as the Multi-Star or Blitz Cannon. As soon as ammo crates appear, immediately smash them so the Mutant Protopet does not get them, and when a small, round bomb appears, use the Tractor Beam to control it and move it into the Mutant Protopet, denying it of the bomb and also giving you a powerful weapon against it.
When it loses a third of its health, it will roar in pain and smash the platform, dropping you down to the lower platform, with Megacorp Trooper v2.0s defending it. Use the Kilonoids or Megaturret Glove to deal with any smaller enemies, but otherwise focus all firepower on the Mutant Protopet. After it loses another third of its health, it will drop down to final platform, with Megacorp Hover Tanks circling the platform and firing at you. Because of the size of the arena, their slow bullets, and the camera forcefully focusing on the boss, it can be easier to just ignore them entirely and just dodge their fire and focus on the Mutant Protopet. Proceed to take out the final portion of its health, completing the mission and finishing the game, plus allowing you to enter challenge mode