The game's plot is based on the 2007 film TMNT, but is told in the form of a flashback by the Turtles and Splinter.

After having defeated their prior arch-nemesis, the Shredder, the Turtles have grown apart as a family. Leonardo had traveled to Central America to improve his ability as a martial artist, and as a disciplined leader. He also obtains a mysterious medallion.

In Leonardo's absence, the remaining the three Turtles go their separate ways. Raphael adopts a vigilante-styled persona known as the Nightwatcher, Michelangelo gets a job as a children's birthday party entertainer (or punching bag), and Donatello becomes a telephone computer-support assistant.

When Leonardo comes home from his long venture, there is immediately strain in his relationship with Raphael.

While Leonardo and Master Splinter endeavor to heal their family's bonds, mysterious Foot Clan activity and monster sightings cause additional difficulty.