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. Donatello gets one of the broken Mousers working and the Turtles chase it through the sewers. Meanwhile, Stockman's lab assistant April O'Neil uncovers a secret subterranean facility where hundreds of Mousers are being manufactured and stored - but to what end?

Raphael is a little cooped up underground with only his brothers and Master Splinter. When Raphael almost clobbers Michelangelo in some brotherly sparring, it's apparent that Raphael needs to get out let off a little steam. But when he meets up with Casey Jones, a vigilante erring a little to the right of justice, Raphael must face the reality of his own hothead ways.