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A year after the attack on April's apartment and shop, the Turtles return to New York to fight the Shredder.
Tensions are running high amongst the brothers, Raphael wants to finally return to the City, but Lenoardo feels it is not time yet. The two Turtles engage in a fierce fight, when it is over, Raphael takes off on his own towards the city. While there he finds the foot clan circling around the Turtles former home in the sewers. Eventually his 3 brothers decide to join him, and catch up with Raphael in their old home, only to find Raph there already with a Triceraton warrior, known as Zog.
With Zog's help the Turtles find where the foot clan are hiding and invade them. During the battle Zog is killed, and the Turtles finally come face to face with Shredder.
Seperate from his brothers, Leonardo faces off with Shredder alone, in their final battle. He is seeking revenge after being attacked while out on a training session durings Shredders last attacks, he was nearly killed, before the TMNT escaped to the country side.
The Shredder is revealed to have been brought back to life by using colonies of worms to inhabit the leftover remains of the Shredders body from his original fight with the Turtles.
Leonardo finishes off Shredder, decapitating him after a long fight.
Afterwords the Turtles set Shredders body ablaze and leave him on a barnacle floating across the New York Harbor.