Through contact with a mysterious ooze, four turtles in the sewers of New York mutate into intelligent pizza-loving humanoids, and are mentored in the art of ninja combat by the wise rat Splinter. When the evil Shredder attempts to take over the world, the turtles set out to stop him.
The Turtles continue to live in the shadows and no one knows they were the ones who took down Shredder. Vernon is the one everyone thinks is the one who took Shredder down. April O'Neill does some snooping and learns a scientist named Baxter Stockman is working for Shredder. He plans to break him out while he's bringing transported. April tells the turtles, who try to stop it but can't. Stockman tries to teleport Shredder but he some how ends up in another dimension and meets a warlord named Krang who instructs Shredder to assemble a teleportation device he sent to Earth a long time ago. He gives Shredder some mutagen which he uses to transform two criminals who were also in the transport with him, Rock Steady and Bebop, into mutants. They then set out to find the device. April saw the transformation while investigating Stockman. She takes the mutagen and is chased by Shredder's minions, the Foot Clan. She is saved by a man named Casey Jones who was the one transporting Shredder. The Turtles show up and they try to work together. In the melee, the mutagen ends up with the police. Knowing Shredder will try and get it back, April tries to get it first and she asks Vern to help. Eventually she and Casey are arrested. The Turtles get the mutagen and Donatello analyzes it, learns it could make them human, which he tells Leonardo who tells him to forget it and not to tell the others. But Michelangelo tells Raphael who feels that Leonardo doesn't respect them.
Darkness has settled over New York City as Shredder and his evil Foot Clan have an iron grip on everything from the police to the politicians. The future is grim until four unlikely outcast brothers rise from the sewers and discover their destiny as Teenage Mutant Ninja Turtles. The Turtles must work with fearless reporter April O'Neil and her cameraman Vern Fenwick to save the city and unravel Shredder's diabolical plan.