The Turtles discover the source of the Mouser robots that trashed their old lair: Dr. Baxter Stockman -- a noted technological genius/inventor, who tries to pass off the Mousers as a means to eradicate the city's rat problem.

Believing the Turtles can accomplish so much more for the city, and inspired by iconic superhero Silver Sentry, Michelangelo decides to take a crack at being a superhero.

Michelangelo's quest to collect a rare comic take the TMNT and Casey Jones back to Northampton, Massachusetts. Here they uncover a plot by a madman to kidnap the members of a retired super-hero team called The Justice Force.

The Battle Nexus tournament begins to take it's toll on the TMNT : Leonardo is poisoned, Splinter is framed, and Lord Draco moves closer to victory.

The Turtles and Splinter find themselves in a futuristic world after accidentally being pulled through a time window.