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As a crime wave rises in New York City, reporter April O'Neil correctly theorizes that the mysterious ninja Foot Clan is behind the rising chaos. The Shredder, the Foot leader, orders April silenced. She is attacked by the Foot in a subway and knocked unconscious. Raphael, one of the Teenage Mutant Ninja Turtles, emerges from the shadows, defeats the Foot, and carries her to the turtles' hideout, unaware that one of the Foot is following him. Splinter, their rat master, explains to April that he and the turtles were once ordinary animals, but were mutated into intelligent creatures by toxic waste, and trained by Splinter in the art of ninjutsu. After the turtles escort April home, they find their hideout ransacked and Splinter kidnapped. They return to April's apartment and spend the night there.
Danny Pennington, the delinquent son of April's supervisor Charles Pennington, works for the Foot. After bailing Danny out of jail for robbery and truancy, Charles stops at April's apartment where Danny glimpses one of the turtles hiding. He reports this to the Shredder.
After an argument with Leonardo, Raphael goes to the roof of April's apartment building, where the Foot ambush him. He is knocked unconscious and the turtles scramble to defend themselves, assisted by the vigilante Casey Jones, who had recently met Raphael. The building catches fire during the fight and the turtles retreat to an abandoned farm belonging to April's family. Raphael recovers and the turtles train while April and Casey fall in love. Leo contacts Splinter through astral projection, and the turtles return to New York to rescue him.
Danny has secretly been taking counsel from Splinter, who tells him the story of his master Hamato Yoshi's murder by a rival ninja, Oroku Saki, over the love of a woman named Tang Shen, while Splinter was an ordinary rat. During the struggle, Splinter's cage was broken and he lunged at Saki's face, clawing and biting him. Saki threw Splinter to the floor and took one swipe with his katana, slicing Splinter's ear. When Danny learns the Shredder intends to have Splinter killed, he and Casey set him free. Splinter reveals to the other teens who have been recruited by the Foot that the Shredder has been brainwashing them to do his dirty work. Realizing this, they all resign from the Foot.
The turtles engage the Foot in battle, easily defeating every Foot Clan ninja, but upon facing the Shredder, he defeats them singlehandedly. As the Shredder prepares to kill Leonardo, Splinter appears and challenges him to a fight. Splinter names Shredder as Oroku Saki; Saki removes his mask and touches his scar, remembering how Splinter gave it to him. He charges Splinter to spear him, who ensnares the Shredder's yari with Michelangelo's nunchaku, leaving him dangling over the roof's edge. In a final attempt to kill Splinter, Shredder throws a tanto at Splinter, but when Splinter reaches to catch it, his grip is released and Saki falls into a garbage truck. Casey pulls the lever "accidentally" to activate the compactor, crushing the Shredder. As the police and media arrive and arrest the Foot soldiers, the teens tell them the location of the Foot hideout. Charles is reunited with his son Danny and gives April her job back. Reunited with Splinter, the turtles watch as April and Casey kiss.
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