The camera pans over an aerial view of New York City as news reporter April ONeil (Judith Hoag) covers a story about a string of mysterious, and seemingly organized, thefts occurring across the city. We see various scenes of members of the gang, known as the Foot Clan, stealthily stealing various items from people right under their noses. As April walks across a vacant lot at the end of the day, she stumbles on a group of thieves stealing merchandise from a van. They pin her to the ground and attempt to steal from her when, suddenly, the single light in the lot goes out and, by the time a nearby police unit arrives, the thugs have been tied up. April finds a sai lying on the ground and puts it in her purse as a mysterious pair of eyes watches her from under the lid of a manhole. The figure curses under his breath before disappearing underground.Deep in the sewers, a unique silhouette introduces the main titles before four humanoid turtles wearing colored eye-bands appear, cheering in celebration. They return to their home where their master, a large rat named Splinter (voiced by Kevin Clash), asks if they were seen and recites to them the importance of their continued training as ninjas (while one of them orders out for pizza). His attempts to meditate are interrupted when one of the turtles turns on the radio and they all start partying, except for one. The turtle with the red eye-band, Raphael (voiced and acted by Josh Pais), already irritated by the loss of his sai, announces that he's going out to a movie, wearing a trench coat and hat as a disguise. In the meantime, two of the turtles, Donatello (in purple, voiced by Corey Feldman and acted by Leif Tilden) and Michelangelo (in orange, voiced by Robbie Rist and acted by Michelan Sisti), wait for the delivery man (Michelan Sisti) and skimp out on paying full price for a 2-minute-late pizza.While out, Raphael manages to trip up a couple of thugs trying to steal from an old woman. As they run into a nearby park, Raphael follows them and meets a vigilante who introduces himself as Casey Jones (Elias Koteas), wearing a hockey mask and armed with baseball and cricket bats. Casey and Raphael get into an argument over the proper way to deal with the thugs and fight each other instead, ending with Raphael in a garbage can and fuming over being called a freak. Casey escapes and Raphael returns to the sewers where his temper is calmed with kind words from Splinter.The next day, April pays a visit to the chief of police after a report where she is criticized by Chief Sterns (Raymond Serra) for putting her nose into his business regarding the supposed organized crime wave. She walks to the subway to go home and is confronted by a team of thieves dressed in concealing ninja garb. The leader (Leif Tilden) slaps her across the face and tells her to keep her mouth shut about the Foot. When she tries to fight back they knock her out but are attacked by Raphael in disguise. The Foot leader comes to in time to see Raphael carrying the unconscious April down the subway tunnel and follows them. Raphael takes April to the turtle's hideout, to everyone's disapproval. The Foot leader peeks in through the doorway, sees the turtles, and retreats. When April wakes up, she screams at the sight of the turtles and of Splinter who proceeds to explain who they are and why they're here.Apparently, fifteen years prior, Splinter had been living in the sewers after being separated from his master, Hamato Yoshi, when he discovered four baby turtles that were moving around in some kind of toxic waste. He herded them to his home where they quickly grew larger, eventually walking on two feet and talking. Splinter noticed changes in himself as well, 'particularly in intellect', and began training the turtles in what he knew of the martial art of ninjutsu. He gave them names, reflecting on famous Renaissance artists: Raphael (in red), Leonardo (in blue, voiced by Brian Tochi and acted by David Forman), Donatello, and Michelangelo. Each turtle also has his weapon of choice: Raphael wields two sai, Leonardo practices swordsmanship with twin ninjato, and Donatello favors the bo while Michelangelo prefers two nunchaku.The turtles escort April home and spend some time with her, at the expense of some frozen pizza. When they return home, they find their lair broken into and Splinter missing. With nowhere else to go, they return sullen to April and spend the night in her apartment.Danny Pennington (Michael Turney), a teenage thief seen earlier in the film, is released from jail the next morning to his father, Charles (Jay Patterson), as part of a deal with Chief Sterns. Since Charles is head of Channel 3 news, Sterns releases Danny on the condition that April cease her harsh coverage on the Foot. Charles stops by April's apartment that morning and advises her to stop running her story before it gets her into further trouble. April, however, is more concerned about Charles discovering the turtles hiding around the apartment. Danny spots one briefly through a reflection before he and his father are ushered out. While driving home, Charles confronts Danny about stealing and when he stops in traffic Danny gets out of the car and runs away. He goes to an abandoned warehouse near the harbor which the Foot has claimed as its base of operation. Teenagers from across the city unload stolen items or play games under the watchful eye of Tatsu (Toshishiro Obata, voiced by Michael McConnohie) who is second in command. A gong signals a mass meeting and everyone gathers in a large arena where their leader, Master Shredder (James Saito, voiced by David McCharen), a man clad in menacing ninja armor, addresses them as his outcast children. He tells them of a new threat to their order as Splinter, tied up against a wall in the back, listens. Upon mentioning the word 'turtles', Danny speaks up.At April's apartment, the turtles watch the news as April updates on recent thefts and sends out a personal thanks to Raphael for rescuing her. However, Raphael and Leonardo soon get into a heated argument over what to do with Splinter gone and Raphael leaves the apartment. He goes to the roof where he's ambushed by an army of Foot Clan ninjas. He is thrown, unconscious, back into April's apartment just after she gets home and the turtles are forced to fight. They all wind up in the antique shop below and are soon outnumberd as Tatsu arrives with reinforcements. However, Casey Jones suddenly appears, having spotted Raphael from the rooftops earlier, and helps the turtles escape through a secret doorway as the building catches fire. They escape in April's van and the ninjas retreat as the shop and apartment burn to the ground. Danny watches from afar.They decide to hide out at a farm that belonged to April's family and everyone pitches in to make the place more livable. Raphael remains unconscious and Leonardo provides an endless vigil. April recounts what happens in a diary and draws sketches of the turtles while trying to resist the charm that Casey puts on her. Once Raphael comes to, the turtles reconcile and resume their training. Despite their absence from the city, Shredder is bent on finding them, telling Tatsu that their method of fighting reminds him of the past. While meditating, Leonardo manages to make contact with Splinter and convinces the others to join him in a seance that night. They all share a vision of Splinter who tells them how proud he is and that they have mastered training of the mind; becoming true ninjas, before disappearing. The turtles decide to return to New York to find and rescue him.At the Foot Clan warehouse, Danny discovers Splinter who detects Danny's confusion and angst and speaks to him. He offers Danny guidance and advice during their short conversations, telling him once that 'all fathers care for their sons', despite Danny's anger towards his father.The turtles return to their lair and find Danny hiding out in a closet. He tells April he ran away from his father but will go back to him if he could just spend the night. Everyone agrees to let him stay and April shows and gives him one of the drawings she did of the turtles. During the middle of the night, Danny abruptly leaves, but not before drawing the attention of Casey, who follows him. They go to the Foot Clan hideout where Danny, confused, seeks out Splinter while Casey knocks out a Foot ninja and steals his outfit.Danny goes to Splinter who tells him of his time living in Japan with his master Yoshi. Splinter imitated his master's practices of ninjutsu, in which Yoshi competed with a man named Oroku Saki. Both men also competed for the love of a woman named Yang Chin, but Chin loved only Yoshi and, instead of seeing him fight for her hand, convinced him to flee with her to America. However, Saki followed them and quickly dispensed them both in a rage. Splinter escaped from his cage and leapt at Saki's face, scarring it. Saki swung at Splinter, slicing part of his ear, before disappearing. Danny asks what became of Saki to which Splinter replies that no one truly knows, but Danny wears his emblem on his head band. Shredder discovers the two, asking where Danny's been before removing the drawing from his back pocket. He angrily walks away to gather his forces and tells Tatsu to kill 'the rat'. Hearing this, Danny rushes back where he runs into Casey and explains that they have to rescue Splinter. They manage to get him out of his chains but are stopped by Tatsu and a team of ninjas.Meanwhile, the Foot sets out to ambush the turtles in their hideout but are surprised by a sneak attack. The turtles fiercely fight back and bring the conflict to the streets above where they eventually wind up on a rooftop. As they fight, Casey engages Tatsu in one on one combat and manages to overpower him. Before leaving, he questions the gang members on their idea of this so-called family that they're a part of.After dispatching a few remaining ninjas, the turtles are surprised by the sudden appearance of Shredder who engages the turtles in combat, but they prove to be no match for him. When the turtles ask about Splinter, Shredder mocks them and implies that Splinter is dead. Furious, Leonardo rushes him only to be pinned. The other turtles are forced to throw down their weapons. Before another blow can be struck, Spinter appears on the roof and speaks out to Shredder, addressing him as Oroku Saki. Shredder charges Splinter with a yari but is flipped over the roof by Splinter's quick movements, using one of Michelangelo's discarded nunchaku. Using the coil of the nunchaku, Splinter holds Shredder by his yari precariously over the edge of the roof. When Shredder throws a knife at him, Splinter releases his grip, causing Shredder to fall into the compactor of a garbage truck. Casey casually flips a switch and the hydraulic door closes, crushing Shredder's mask.The turtles reunite with Splinter as police arrive on the scene and question the remaining Foot members who reveal where all the stolen goods are kept. April prepares to run a final update on the story when news crews arrive and gives Casey a celebratory kiss. The turtles cheer and exchange slang exclamations before Splinter says that his favorite has always been 'cowabunga'. The turltes unanimously agree and cheer as Splinter laughs, saying he 'made a funny', and the film ends.