When the New York City Police Department is unable to stop a severe crime wave caused by the Foot Clan, four vigilantes — Leonardo, Michaelangelo, Donatello and Raphael — come forth to save the city. Under the leadership of Splinter and together with their new-found allies April O'Neil and Casey Jones, they fight back and take the battle to The Shredder. The film kept very close to the dark feel of the original comics, and is a direct adaptation of the comicbook storyline involving the defeat of Shredder, with several elements also taken from the animated series that was airing at the time, such as April being a news reporter, and the turtles having different-colored masks, as opposed to the uniform red masks of the comic. The film was the highest-grossing independent film of all time when it was released, and became the ninth highest grossing film worldwide of 1990 and the most successful film in the franchise.
As an unsolved crime wave rises in New York City, news reporter April O'Neil covers the reports and rumors of a mysterious 'Foot Clan,' a gang of ninjas that is plaguing the city. April continues to cover news of the crime wave, to the point where the Shredder, leader of the Foot, decides she needs to be silenced. She is attacked by the Foot in a subway and is knocked unconscious while trying to fight them off. Raphael has been following her to retrieve his sai - which he had lost in a previous battle - and easily fights off the Foot. He carries April back to the Turtles' hideout, unaware that he is being followed by one of the Foot. Splinter then recounts to an astonished April his and the Turtles' origins: once ordinary turtles living in the sewer, they were mutated into intelligent, human-sized creatures by a discarded canister of toxic waste. The Turtles escort April back home. Upon their return to the sewers, the Turtles find that their home has been ransacked and Splinter kidnapped. With nowhere else to go, the four distraught Turtles return to April's apartment and spend the night there.
Meanwhile, the Foot Clan continues to grow, incorporating a number of delinquent teens into their ranks. One of these teens is Danny Pennington, who is arrested for robbery. After bailing Danny out of jail, his father and April's supervisor Charles Pennington stops by her apartment, where Danny incidentally catches a glimpse of one of the Turtles in hiding. He then reports back to the Shredder, who has been searching for the Turtles.
At April's apartment, Leonardo and Raphael get into a heated argument. Raphael goes to the roof of the building, where he is ambushed by an army of Foot Clan ninjas. He is thrown unconscious through April's skylight, and the Turtles scramble to defend themselves from the Foot. Things look bleak until the arrival of Casey Jones, who helps them fight off the remaining Foot warriors. However, the building catches fire during the melee, and the Turtles have no choice but to retreat.
They retreat to a farm that belongs to April's family, and she learns that she was fired from her job. Raphael eventually recovers from his coma, and the Turtles train together vigorously, while April and Casey fall in love. At one point, Leonardo manages to make contact with Splinter through meditation, and after the Turtles witness him in a shared vision, they decide to return to New York to find and rescue him.
Despite being a member of the Foot Clan, Danny had secretly been taking counsel from Splinter, who shares with him the story of his master Hamato Yoshi's murder by a rival ninja named Oroku Saki. Splinter explains to Danny that during his master's scuffle and murder at the hands of Saki, the cage that he stayed in had been knocked over. After being freed from the cage he lunged at Saki's face. Grabbing on with his claws he proceeded to bite and claw Saki's right cheek. Saki, bleeding and enraged, knocks Splinter to the floor and slices off part of his ear with his katana. When Danny learns that the Shredder intends to have Splinter killed, he and Casey set him free from captivity.
Although the Foot were set to ambush the Turtles in the sewers upon their return, the Turtles manage to turn the tables on them. The fight escalates into the streets above and eventually onto a rooftop, where the Turtles finally face off against Shredder, but prove to be no match for him. Leonardo eventually scores a hit with his ninjato, but is ultimately disarmed and pinned to the ground. Before Shredder can finish Leonardo off, Splinter appears and challenges him to a fight. Splinter reveals to the Shredder, he knows he is in fact Oroku Saki, and that they met many years ago at the home of Hamato Yoshi. Splinter challenges him to remove the cowardly mask that he has been using to hide his shameful wound. Saki removes his mask and touches his scar, remembering how Splinter gave it to him. Saki then charges Splinter, who using Michelangelo's nunchaku, ensnares the Shredder's yari, leaving him to dangle precariously over the roof's edge. In desperation, the Shredder throws a tanto from his belt, but when Splinter reaches up to catch it, his grip is released and Saki falls into the back of a garbage truck. Casey then pulls the lever to activate the compactor, crushing the Shredder. As the police arrive on the scene, the teens inform them on where all the stolen goods can be found.
On the roof, the Turtles reunite with Splinter and, while trying to come up with a proper word to cheer with, Splinter suggests the phrase "Cowabunga." The Turtles unanimously agree, and Splinter declares, "I made a funny!" as the film ends.
- Judith Hoag as April O'Neil
- Elias Koteas as Casey Jones
- David Forman as Leonardo
- Michelan Sisti as Michaelangelo
- Leif Tilden as Donatello
- Josh Pais as Raphael
- James Saito as The Shredder
- Michael Turney as Danny Pennington
- Jay Patterson as Charles Pennington
- Raymond Serra as Chief Sterns
- Toshishiro Obata as Tatsu
- Sam Rockwell as Head Thug
- Brian Tochi as Leonardo
- Robbie Rist as Michaelangelo
- Corey Feldman as Donatello
- Josh Pais as Raphael
- Kevin Clash as Splinter
- David McCharen as The Shredder
- Michael McConnohie as Tatsu