After rescuing Professor Jordan Perry from Shredder and the Foot Clan, the Turtles take him back to their hideout so he and they could figure out a way to defeat Shredder's super-mutants, Tokka and Rahzar. They develop an anti-mutagen which needs to be ingested, so Donatello solidifies them into ice cubes and has them put in donuts. In an encounter between the Turtles and Tokka & Rahzar, they give them the donuts, and each eat one before they find the cubes in them. Tokka & Rahzar proceed to whup their butts right into a Vanilla Ice concert, and due to the anti-mutagen began emitting disgusting burps.
Professor Perry finds Donatello and tells him that carbon dioxide was essential for the anti-mutagen to work, and their burping was retarding the reaction. So, in order to speed it back up, the Turtles use fire extinguishers, because a chemical in them would do the trick in speeding up the process. They manage to incapacitate Tokka and Rahzar and jam the fire extinguisher's smoke down their gullets, eventually causing them to transform back into a regular wolf and snapping turtle. The Turtles then dispose of some more Foot Clan members, dance for everyone, and then dance on stage with Vanilla Ice before Shredder shows up, can of ooze in hand, and tells them the war isn't over so long as he possesses that. Keno then shows up and spin kicks the can out of Shredder's hand, which Professor Perry collects, escapes with, and later disposes of. Shredder then tries to escape by taking a female concert-goer hostage and threatening to use a small vial of ooze on her if anyone followed, but Donatello pumps the speakers to full volume, and as Keno distracts Shredder, Michaelangelo hits a guitar synth hard, and the sound knocks Shredder through the air out of the concert hall and into the dockyard.
The Turtles, after lambasting Keno for getting involved in a fight that wasn't his, go outside to see where Shredder landed, but can't find him. Thinking they vanquished him, they celebrate, but then a now-mutated Shredder (Kevin Nash), thanks to drinking the last vial of ooze, brings them down underneath the dock and starts tearing the dock's foundations apart. The Turtles escape into the water before Shredder brings the last of the dock's foundations down, and Shredder is crushed beneath the debris. The Turtles emerge, and see Shredder's hand emerge from the wreckage, but it soon falls limp, indicating his death.
The Turtles return home victorious, only to find out their stealthiness had been compromised at the concert through a newspaper Splinter shows them, and they are told to do ten flips as punishment.
Thanks Tornado Dragon!