In the two-part second-season finale "The Invasion", Shredder and Kraang Prime formed a full alliance in which Shredder and the Foot Clan will help the Kraang take over New York and then the world and in turn, the Kraang would return Karai to normal, and deliver Splinter and the Turtles to him. Later, he watched as Leonardo fought and eventually defeated his army of Foot Bots, after which he sent Rahzar, Fishface, and Tiger Claw to take care of him. Leonardo managed to subdue them for a short period of time before Shredder got involved and badly injured Leonardo. Later, Splinter confronted him and the two battled until Splinter got trapped under large metal pipes. Shredder was prepared to kill his rival once and for all; however, Leatherhead intervened, and was defeated when Shredder sliced the front of his torso and kicked him off the edge of the dock. Splinter became furious as he broke out from under the pipes and tackled Shredder to the sewers. Later, the Turtles (minus Leonardo) and April watched helplessly from behind metal bars as Shredder defeated Splinter and seemingly killed him by throwing him down a large draining bay.