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Protopets are Megacorp's genetically-modified pets. Protopets were originally designed to be the ultimate pet, however the experiment had numerous sideeffects and the project was almost abondoned. But Megacorps owner, Abercrombie Fizzwidget decided to release the dangerous pet to the public even with its flaws. The protopet was then shipped around the Bogon Galxy and sold as the Ultimate pet.
The Protopet, dubbed "Experiment #13" during its testing stages, showed extreme violence eating many of the scientists working on the project. Angela Cross, one of the leading minds of Experiment 13 quit when the pet was released and became "The Thief". She tried to stop the protopets by reprogramming their brains from the Megacorp HQ. Then the protopet was stolen by the thief prior to its intended release, so "Fizzwidget" hired Ratchet and Clank to recover the creature. They eventually did so, not realizing the conspiracy at hand. The pets were soon released to the public despite warnings from Megacorp's scientists, most of whom were devoured by the original Protopet during testing. It became clear that their sole purpose was to consume other sentient life, be it organic or even robotic.The protopets also spread incredibly quickly producing more protopets every minute.
The released pets began to attack people all over the Bogon Galaxy, causing chaos across numerous worlds. Ratchet has to fight these cute but deadly cretures throughout Going Commando. Several planets, among them Grelbin and Damosel, were quickly infested by the Protopets, threatening social order and prompting the intervention of local authorities.
Ratchet and Anglea finally reach the Main control room of Megacorp only to be confronted by Fizzwidget who then revealed himself as being Captain Qwark. Qwarks plan was to let the galaxy be terrorised by the protopetts and then, at the last minute use the device that can make the protopets harmless, returning him to his former fame and glory. However. Qwarks plan went wrong and the result was The Mutant Protopet. The mutant then devoured Qwark and Began rampaging through the facility. Ratchet has to defeat the Mutant Protopet as the last boss of the game.
After Ratchets victory, Angela quickly fixes the device that Qwark had broken rendering all protopets int the galaxy harmless, making them into the perfect pets they were originallt designed to be.
It is unknown how their previous rampage across the galaxy affected later sales of the Protopets.