The only universe in which The Shredder is definitively slain is in the Mirage Comics. He is killed in issue 1 of volume 1. After defeated by the Turtles, he refuses honorable suicide, instead choosing to attempt to blow up the entire rooftop with a thermite grenade, killing the Turtles along with himself. Donatello throws his bo like a javelin, hitting Shredder and knocking both him and the grenade off of the roof. The grenade goes off in proximity to Shredder, killing him.