Darwin finds a classified file titled Clusterstorm on Saber’s personal computer, containing plans for global extermination, and downloads it to his PDA. However, the next day, the file turns out to be false, which angers Ben’s superior, Agent Kip Killian, who shuts down the program. He orders the animals’ capture, forcing Darwin, Blaster, Juarez, and Speckles to escape and hide in a delivery truck that goes to a pet store where they are mistaken for ordinary rodents and are locked up in a cage. They meet Hurley, another guinea pig, Bucky, a cocky hamster, and three mice. Determined to finish their mission, each of them forms an escaping plan. Blaster and Juarez get themselves sold to a family, while Speckles pretends to be dead to get buried, but is thrown into a garbage truck instead, seemingly crushed to death.