In "The Noxious Avenger", Bebop and Rocksteady were tasked by Stockman to retrieve a chemical known as "Reagent-X" (and some groceries, to their anger) in order for to create a mind control serum for Shredder to use on Karai, inadvertently finding some mutagen in the process. During their battle with the Turtles however, the mutagen they found wound up being thrown by Zeck all over humble sewer worker-turned-garbage man Garson Grunge, who mutated into Muckman. After witnessing him defeat the Turtles in a later encounter, Bebop and Rocksteady took advantage of the lost and confused Muckman, by convincing him that it was the Turtles' doing for his mutation. Muckman then temporarily helped the duo steal another chemical fighting the Turtles, but eventually came to his senses after noticing Bebop and Rocksteady's true nature when the Turtles rescued him, thus turning on them and destroying the chemical, which caused Bebop and Rocksteady to retreat. In "Meet Mondo Gecko", the two attended Xever's underground mutant race with the rest of the Foot and other mutants who were foes of the Turtles. In "The Deadly Venom," a mind-controlled Karai was able to defeat Rocksteady in combat as part of a test to see if the mind-control serum worked on her.