Having guarded April O'Neil on her journey home from the Hidden Leaf Village, the Teenage Mutant Ninja Turtles and Team 7 are ready to relax, pick up some dinner, and call it another successful mission. The bright city lights of Big Apple Village cast dark shadows, though, and when they return to the Turtles' lair, it's been ransacked. April and Splinter are gone, and there's only one person who could be responsible. Naruto, Sakura, Sasuke, and Kakashi must help save both their missing comrades and April's sample of mutagenic ooze before it's too late, or Shredder's single-minded pursuit of power won't just threaten one village, but them all.