At the beginning of a very normal day in the sewer Michaelangelo is skateboarding through various tunnels. As he is making his way along he begins to notice a trail of dead rats leading into a tunnel. He investigates and discovers a pool of red ooze rushing towards him killing everything its path. He quickly turns to skate back to the Turtles hideout only to be knocked over the head and dragged away.
Waking up Michaelangelo discovers he is being held by a group of mutants who live in the sewers known as the Morlocks. Their leader Callisto begins to question him about why he is poisoning the sewers. Michaelangelo quickly begins to explain that he is also a mutant created when an ooze coats him and his brothers. He tells them the history of the turtles and how they are constantly protecting New York from the evil Shredder and his Foot clan.
Callisto releases Michaelangelo and tells him of the Mutants struggle to survive and of the man Henry Gyrich who wants ti kill all mutants. Together Callisto and Michaelangelo decide that two teams are needed to combat this problem. Michaelangelo will gather his brothers and attack discover who us behind the red ooze, while the Morlocks will attempt to shut the ooze off at it's source.
Michaelangelo meets back with his brothers and explains what is happening. Donatello is able to use his computer to track who is creating the ooze, a company operated by Henry Gyrich and The Shredder. The Turtles infiltrate the facilitie creating the ooze an attempt to stop Gyrich and The Shredder. While battling with the two Villians they are able to defeat them but not before Gyrich releases all of the remaining ooze into the sewers killing both The Morlocks and The Foot clan in one tragic moment.
The Turtles return home crushed by the magnitude of their failure to protect their home and the Morlocks. They attempt to salvage something from the loss by fighting for mutant kind and join The Brotherhood of Mutants in an attempt to ensure that all those who would hurt Mutants will suffer and that what happened to the Morlocks never happens again.