Bebop and Rocksteady use Krang's new Mutagen on Bebop's pet turtle Slash so he can do their housework for them. Slash runs away and is conned by an irritated entrepreneur into framing the TMNT.

After many failed attempts from his rodent subjects to find food, the Rat King learns of an abandoned canister of mutagen lost in the sewers and claims it for himself. Then, he kidnaps Irma and Vernon and uses the mutagen to transform them into his mutant slaves, for the sole purpose of raiding food warehouses. It is later discovered that the mutations are unstable and can only be active if the Rat King plays his hypnotic flute.