The mutant outbreak continues to spread throughout the sewers and subway tunnels while the Turtles try to contain the threat. Back at Area 51, Baxter Stockman prepares a new body for cerebral transfer despite warnings from Agent Bishop. When Stockman's body begins to show signs of rejection, he becomes delirious, which leads to a rampage against the person he believes to have caused all his problems, April O'Neil. In the end, seeing April as his mother due to his delusions, Stockman sacrifices himself by being drowned in the East River while handing her to the Turtles and Casey. This episode was initially banned from airing on US television due to content issues.

Whoa, dude! Worlds collide when the Turtles from one dimension meet the Turtles from another dimension! What the shell is going on? The two Turtle teams must work together to find the Technodrome and undo this multi-dimensional mess! Meanwhile, Shredder sets out to track down his counterpart, Ch'rell, who devises a master plan to travel back to the Prime Universe to wipe all the Turtles out of existence! Get ready for two times the Turtle Power as the teams seek guidance from two versions of Splinter, meet classic characters like Casey and April, and face a slew of enemies!

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.