During a night of showing off their extreme sports gear, the Turtles are attacked by a monster from beneath the Earth. They trace the beast to a remote island where they uncover their old foe, Dr. Baxter Stockman, who has created vicious monstrosities to unleash on the unsuspecting public.

Starting March 7, 2009, a series of 13 shorts, called "chapters," ranging from 90 seconds to two minutes in length began airing on The CW4Kids during episodes of TMNT: Back to the Sewer and Chaotic: M'arrillian Invasion, as well as being streamed on the 4Kids website a week in advance of airing on television. They comprise a single story called "Mayhem from Mutant Island."[7] On March 27, 2010 the 13 shorts were re-aired edited together under just the "Mayhem from Mutant Island" title as a so called "new" episode of TMNT: Back to the Sewer.