In the second season, Shredder left the New York clan under Karai's command, citing urgent business to attend to in Japan. Karai, having been lied to by Shredder to believe that Splinter killed Tang Shen (believing herself to be Saki and Shen's child), uses her new position to aggressively hunt the Hamato Clan until her father's return. Shredder reshuffles the Foot Clan's hierarchy upon his return, installing mutated Japanese mercenary Tiger Claw as his new second-in-command and stripping Karai of the position, though Tiger Claw was briefly trapped in various other dimensions before eventually returning to the fold. Baxter Stockman was later mutated into Stockman-Fly upon his mutagen collar being set off by Shredder for his 74th attempt at making a mutant army for him. However, having been told of her true nature by Splinter and the Turtles, Karai betrayed her father, and when she was brought before him, he admitted that she was Splinter and Tang Shen's biological daughter and imprisons her. The Foot Clan would on one notable occasion be fully mobilized when the Kabuto was stolen by professional thief Anton Zeck on behalf of Steranko. Karai was soon used in a hasty plan to gain vengeance on Splinter by Shredder, resulting in her mutation into a snake-like mutant (though she went back and forth to an additional chemical that Stockman-Fly accidentally added), further strengthening the violent split between the Foot Clan and the Hamato Clan.