Whilst training in the lair, the TMNT are ambushed by a hoarde of mousers, the resulting conflict destorys the lair,, and the Turtles are seperated from their mentor, Splinter.

As they journey through the sewer network in an effort to reach the surface and locate Splinter, the Turtles do batle with not only further Mouser forces, but also an elite group of ninjas known as the Purple Dragon Gang.