| Clank... You speak nerd.
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The Megacorp Headquarters were a massive facility located on planet Yeedil. It was Qwark's base for operations in Going Commando. It was in this factory that all the Protopets were extracted from the original Protopet. Being Megacorp's latest industrial center, it was heavily guarded by an army of Megacorp's deadliest soldiers.
In order to infiltrate the facility, Ratchet had to activate a teleporter to get inside. Once inside the factory, Ratchet and Clank had to battle against the best Megacorp had to offer. After surpassing all obstacles, they finally reached the Protopet Duplication Room. Angela joined them shortly after, but when they were about to enter the room, Clank's Infobot friend showed them a video, where Captain Qwark had sold his 1,000,000th Personal Hygenator, which would allow him to finance the return of "the greates superhero who ever lived". All that he needed was another galaxy, with new fans, so that he could save them from a new disaster ( the disaster being the Protopet infestation). When the video stopped, Abercrombie Fizzwidget shot the Infobot with a Lancer. He then takes off his disguise, and reveals himself to be none other than Qwark.
Qwark takes Ratchet and Angela into the duplication room, where he poses in front of the cameras, saying that he will stop the Protopet menace and making Ratchet, Clank and Angela Public Enemies Number 1,2 and 3.When he uses Angela Cross's Helix-O-Morph to try and make the protopet harmless, the machine mutates the Protopet into a ferocious abomination, which in turn eats Qwark.
Ratchet and Clank battle the Mutated Protopet and win, saving the day once more. Angela congratulates and kisses Ratchet and Clank. Afterwords, the real Mr.Fizzwidget appears, who Qwark had tied up in a supply closet during the events of the game. Mr.Fizzwidget thanks Ratchet and Clank, but Ratchet regrets not being able to get the Helix-O-Morph back. Suddenly, the Mutated Protopet vomits Qwark, who vomits the Helix-O-Morph. Clank then discovers that Qwark had put the batteries in backwards, and thus it was explained how the Protopet mutated. Angela uses the Helix-O-Morph to cure the Protopets, thus ending the Protopet menace. Ratchet then joins Clank, who is saddened to see his Infobot friend destroyed. Ratchet tells him not to worry because he can fix her, making Clank smile.
- According to the TV Transponder that Ratchet got on Greblin, the Protopets were all extracted from the original Protopet.