As a crime wave rises in New York City, reporter April O'Neil covers the mysterious ninja Foot Clan. The Shredder (Teenage Mutant Ninja Turtles), the Foot leader, orders April silenced. She is attacked by the Foot in a subway and knocked unconscious. Raphael (Teenage Mutant Ninja Turtles), one of the Teenage Mutant Ninja Turtles, emerges from the shadows, defeats the Foot, and carries her to the turtles' hideout, unaware that one of the Foot is following him. Splinter (Teenage Mutant Ninja Turtles), their rat master, explains to April that he and the turtles were once ordinary animals, but were mutated into intelligent creatures by toxic waste. After the turtles escort April home, they find their hideout ransacked and Splinter kidnapped. They return to April's apartment and spend the night there.
One year after the events of the first film, a young pizza delivery boy named Keno inadvertently encounters Burglary on his route and tries to stop them. Seeing him as a witness, the burglars attack Keno, who proves to be an expert Martial artsist, but he is soon overwhelmed before the arrival of the Teenage Mutant Ninja Turtles. They vanish after rescuing Keno, tying the burglars up, and taking the pizza he was delivering, leaving behind the money to pay for it.
In 1603, in feudal Japan, a young man is being chased by four samurai on horseback. As they go into the woods, a mysterious woman emerges from the underbrush and watches closely. However, the samurai eventually capture and take the youth, revealed to be a prince named Kenshin, with them.