Plot
In New York City, shortly after the Teenage Mutant Ninja Turtles defeat the Shredder, a young pizza delivery boy named Keno inadvertently encounters burglars at a mall on his route and tries to stop them. The burglars attack Keno, who proves to be a skilled martial artist, but he is soon overwhelmed before the arrival of the Teenage Mutant Ninja Turtles. They vanish after rescuing Keno, tying the burglars up, and taking the pizza he was delivering, leaving behind the money to pay for it.
Leonardo, Raphael, Donatello and Michelangelo, along with their master Splinter, are currently living with April O'Neil in her new apartment while looking for a new place to live. Splinter wants to remain in the shadows, while Raphael thinks they should live out in the open. At a junkyard where the remnants of The Foot and the Shredder's second-in-command Tatsu are hiding out, they are met by their master, who has been disfigured by his previous defeat and vows revenge on the turtles.
April interviews Professor Jordan Perry of Techno Global Research Industries (TGRI) about a possible toxic waste leak. He assures her that everything is fine, but their scientists secretly discover dandelions which have been mutated by the leak. Freddy, a spy for the Foot Clan posing as April's cameraman, collects one of the dandelions and reports it to his master, who decides to have Perry interrogated. Back at April's apartment, Splinter reveals to her and the turtles that the canister of mutagen (dubbed "Ooze" by the turtles), which mutated them 15 years earlier, was created by TGRI, and they decide to talk to Perry too. The Foot gets to Perry first and kidnaps him, salvaging the last canister of ooze in the process. The turtles ultimately fail to recover the canister. Afterward, Keno gets into April's apartment under the guise of delivering pizza and discovers Splinter and the turtles.
At the Shredder's hideout, Perry is forced to use the remaining ooze on a snapping turtle and a wolf, which mutates them into Tokka and Rahzar, respectively. However, Tokka and Rahzar have the mindset of infants. Shredder considers killing the creatures until Perry points out their enormous strength. With the imminent threat to April's safety by the Foot Clan, the turtles begin actively looking for a new home. After an argument with Leonardo, Raphael breaks off from the group, while Michelangelo discovers the abandoned City Hall subway station and deems it a perfect hideout. Raphael and Keno disregard Splinter's orders and recruit Keno into the Foot Clan to find their hideout. They are eventually discovered, and Raphael is captured, while Keno escapes to warn the others. When they come, they are ambushed by the Shredder and the Foot; Splinter saves the group, but leaves as they face Tokka and Rahzar, who prove too strong to defeat. Donatello finds a bound and gagged Perry after being tossed into a building by Tokka, and the five of them make a tactical retreat. Once back in their hideout, Perry explains that the creation of the ooze was an accident, disheartening Donatello, Leonardo, and Raphael, who saw a higher purpose for their existence.
The Shredder unleashes Tokka and Rahzar into a nearby neighborhood to cause damage. The next day, Freddy sends a message to April that Tokka and Rahzar will be released into Central Park if the turtles don't meet the Foot Clan at the construction site. Perry develops an antidote to the mutations, but it must be ingested to work. When the turtles confront the Foot at the site, they try using donuts to trick Tokka and Rahzar into eating the antidote. Tokka and Rahzar discover the ruse and brutally attack, throwing Raphael into a public dance club where Vanilla Ice is performing. A big fight ensues among hundreds of witnesses. The club owners consider calling the police but see that their customers are enjoying the show. Eventually, the turtles realize that the antidote was giving Tokka and Rahzar gastronomical effects and use fire extinguishers to revert them back to their natural states. Keno arrives as backup, and Shredder appears, taking a female clubgoer hostage. He threatens to use the last of the ooze on her, but is thwarted and sent flying out to the docks. Shredder is transformed into a Super Shredder after consuming the last of the ooze. The heavily mutated Shredder is too strong for the turtles to fight, but they seek refuge in the bay while he rips the dock apart in his rampage, causing it to collapse and kill him.
In a press release, April reads a note from Perry, thanking the turtles for saving him. When they return home, Splinter orders the four of them to do ten flips as punishment for being seen by humans, as evidenced by the morning's newspaper.
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