The Ninja Turtles witness Channel 6 ace reporter April O'Neil being attacked by a group of punks and intervene. However, Raphael loses a sai in the fight, which is picked up and stashed away by April.
After the movie, Raph stops a purse-snatcher and follows him and his accomplice to a nearby park, where he sees a brutal vigilante thrashing the punks. Raph tries to keep the vigilante from going overboard, but ends up losing to him.
Raphael returns home, and is consoled by Master Splinter. Later, as his brothers are watching April on the news, Raph goes out again and stops the Foot Clan from attacking the reporter in the subway. O'Neil is knocked unconscious, and Raph takes her back to the lair. April wakes up and Splinter tries to calm her by telling her their origin. The Turtles then walk her home and accept a pizza as payment.
The Turtles return home only to find their sensei gone. They go to stay at April's apartment, but Raph can't sit still and takes to the rooftop to blow off steam. There, he is ambushed by The Foot, who send him crashing through the skylight, leaving him lying unconscious on the floor.
Aided by the Casey Jones, the vigilante from before who witnessed Raph on the rooftop, April and the other Turtles high-tail it out of the now-burning apartment to April's family farm. After recovering, Raph sharpens his sai and continues to rage about his missing master.
After sensing that Splinter is alive, Leonardo takes his brothers to the forest to summon Splinter's astral form from a campfire. The Turtles, renewed by their father's advice, train until they are ready to go back to the city.
The Turtles crash back at their lair for the night, where they find April's boss' son, Danny hiding there. They all go to sleep for the night, but in the morning, realize Danny is gone with a drawing of Raphael from April's sketch portfolio.
The Turtles head off to fight the Foot, overcoming the rank and file and eventually meeting up with their leader, the insidious Oroku Saki. Saki trounces the teens, but is bested in combat by Splinter and falls off of the rooftop.
Pizza delivery boy Keno is on his way to deliver pizza to the O'Neil home, when he witnesses some thieves robbing Radio Hut at Chet's Mall. He intervenes in an effort to stop them, but is outnumbered - at which point, the Turtles arrive and help take care of the remaining thugs.
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