As an unsolved crime wave rises in New York City, Ash's Aunt April O'Neil (Judith Hoag), reporter for Channel 3 Eyewitness News, covers the reports and rumors of a mysterious 'Foot Clan,' which seems to be the organization that is plaguing the city, much to the ire of Chief of Police Chief Sterns (Raymond Serra), who refuses to acknowledge that they exist. April is attacked in an alley by a group of punks who are quickly taken down when a weapon flies through the air, knocking out the street light. While police are investigating the attack, April finds the sai responsible for knocking out the street light and takes it. One of her rescuers, from the cover of the sewers, watches this and curses himself for his bad luck.
While celebrating, Our Heroes And the four mutated teenage turtles, Leonardo, Donatello, Michelangelo, and Raphael, reunite with their master, Splinter, to recount their first true battle. In a huff, Raphael leaves to go see a movie. After Raph leaves the theater, he chases muggers into the park and encounters Casey Jones (Elias Koteas), a hockey masked vigilante whose brutal attacks on the muggers forces the turtle to stand up for them. After a brief scuffle, Casey escapes Raph, leaving him in a humiliating defeat further fueling his anger. Raph later comes to April's defense after her reports on the Foot Clan draw out a few members who attack her, knocking her out. Raph retrieves his sai and, now at full fighting strength, easily fights them off - unaware that he is leading one of them back to their sewer den. April revives in the den and, after being calmed down, is told the story of Splinter and the Turtles' origins. After some time there, the Turtles head to her home at 11th and Bleecker Street, her apartment home built on top of her family antique store. They spend some time over frozen pizzas telling jokes and stories before they decide they have to head back. Upon their return, the Turtles find that their home has been utterly destroyed and their master taken.
With nowhere else to go, the four return to April's apartment and spend the night. Meanwhile, Sterns discovers that April's boss Charles Pennington's (Jay Patterson) son, Danny (Michael Turney), is in custody, arrested for trying to steal a car stereo, and uses it as leverage to talk to Pennington about other matters. The following morning, Charles warns April not to press any buttons with Sterns, and Danny becomes suspicious when he thinks he sees the Turtles in the apartment. En route to his school, Charles and Danny have an argument and Danny runs away, fleeing to a hideout outside of town where many delinquents and punks have gathered over skateboard ramps, arcade games and other personal pleasures. They are joined into a meeting with The Shredder a man in a black cloak and metal mask who urges them to find the turtles With The Help Of The Bonnie And Clyde Of Gotham City Known As The Joker And Harley Quinn. Danny stands out and relinquishes the location he thinks he saw the Turtles.
April deliberately disobeys Charles' orders and continues to insult Sterns' competency for the job and ignorance to the fact that the Foot Clan exists. After returning home, April gives the turtles a tour of the shop while Raph, after a heated argument with Leo, goes and practices on the roof. He is spotted by Casey, but only seconds before he is attacked by numerous Foot Clan members. Brutally beaten, Raph makes a re-entrance to the house through the skylight window and the turtles fight the remaining Foot members.Seriously outnumbered, things look bleak until the intervention of Casey Jones.Together, they fight off the remaining members of the Foot clan. The building is destroyed, and the group escapes, forcing Tatsu and the Foot to leave. They head to a farm that belongs to April's family, and Casey sparks anger with her when he says he heard Charles' message as they got out of the house that she had been fired for her comments that day. Raph soon recovers from his coma, and the four of them practice until it is time for them to return to New York and find Splinter and reunite their family. Danny meets Splinter and is for the first time in turmoil about his decision to leave his family. Leonardo makes meditative contact with Splinter and for the first time is sure that he is alive. After the four of them each encounter him in a shared vision, they decide to return.
Danny had been living for a few days in the Den and makes formal introductions with the Turtles and Casey. But that night he decides to return to Shredder's hideout and speak with Splinter. Splinter tells him the story of his master Hamato Yoshi being killed by another ninja named Oroku Saki, and Danny realizes that the Oroku Saki is, in fact, Shredder. He overhears Shredder telling Tatsu to have Splinter killed. Danny runs into Casey, who followed him, and the pair face off against Tatsu. After Casey defeats the ninja master, the three of them express the importance of family before leaving.
Meanwhile, the Foot, who had set up an attack against the Turtles at their Den were surprised when they had been ambushed by the waiting Turtles.The fight escalates up into the streets above and eventually up on a rooftop where the Turtles finally face off against Shredder. Shredder easily out maneuvers the four of them in combat, though Leonardo eventually wounds him. He later takes Leonardo hostage in a threat to have the Turtles throw their weapons away. As he is about to kill them anyway, Splinter appears and challenges Saki to a fight. Shredder remembers the old rat who he injured years prior and charges him with a lance. Using a nunchaku that, Splinter dangles Shredder precariously over the roof's ledge.In a final attempt to kill Splinter, Shredder throws a knife, which Splinter catches. However, the rat's grip on the lance is released and the ninja falls into the back of a garbage truck. Casey "accidentally" throws the switch, crushing him in a compactor. Danny pays April back a $20 bill that he had stolen from her earlier and reunites with his father and insists that he be called "Dan" from then on. Charles then pleads April to cover the story offering her a raise and a corner office without breaking a sweat to her demands. Casey approaches her, expecting sympathy for his injuries and trying to flatter her before she gets ready for her interview.April retorts with "Shut up and kiss me, I got a report to do." Casey gladly complies. Upstairs, the turtles reunite with their father figure and while trying to come up with a proper word to cheer to, he suggests the phrase "Cowabunga," a catch phrase from their '80s animated series, concluding with the phrase "I made a funny!" and laughing as the credits roll.
- Ash Ketchum, Pikachu, Ttark, The Joker, and Harley Quinn guest star in this film.
- April O'Neal is revealed to be Ash's aunt and Delia's younger sister.
- The storyline contiunes in Pooh's Adventures of Teenage Mutant Ninja Turtles 2: The Secret of The Ooze and Pooh's Adventures of Teenage Mutant Ninja Turtles 3.
- The TV show The New Adventures of Winnie the Pooh was on ABC Saturday mornings at the time when Teenage Mutant Ninja Turtles was released in theaters in 1990.