After a battle between the Purple Dragons and what appear to be the Teenage Mutant Ninja Turtles is captured on film, the Turtles are quick to refute their master Splinter's accusations of carelessness. Breaking into the Purple Dragons' headquarters to get to the bottom of these mysterious doppelgängers, Pooh And The Others And our Turtles discover that their "impostors" are, in fact, versions of them from another dimension.
The other dimensional "1987 Turtles (Murakami-Wolf-Swenson)" prove to be too childish for the more serious-minded "2003 Turtles (4kids/Nickelodeon)", but they are soon able to discern that they were teleported into their world in a dimensional portal accident that has also brought their arch-enemies, Shredder and Krang, and their battle fortress, the Technodrome, along with them. Pooh, Ash, their friends and The eight Turtles head below the ground to track down the Technodrome, but their presence together only clues Shredder in to the fact that there may be a version of himself on this world that he can ally with to take Our Heroes And the Turtles down.
The Technodrome escapes, and the Turtles, unable to track it, resolve to create a portal device of their own so they can travel to the "1987 universe" and obtain the gear the 1987 Turtles usually use to take the Technodrome down. While the Turtles are occupied with this task, Shredder uses the Technodrome's technology to locate his dimensional counterpart, the Utrom known as Ch'rell, still in frozen exile on an ice asteroid after his final defeat by the 2003 Turtles. Ch'rell is teleported to the Technodrome, but upon recovering, immediately overthrows his bumbling other-self and seizes control of the fortress with the aid of his adopted daughter, Karai, who had been monitoring his movements and tracked him down after realizing he had escaped his frozen prison with special help of Bowser Koopa and his Family(Bowser Jr., Mistress Nine and Ranamon).
Using the Technodrome's technology to create a new robotic exoskeleton for himself, Ch'rell dispatches his right-hand man Hun, who has been mutated into a monstrous mutant turtle himself after being doused with mutagen from the 1987 universe in the earlier battle, to track the Turtles down. With the aid of Bebop, Rocksteady, Bowser Jr. and Ranamon, Hun finds and attacks the Turtles lair, but our heroes and the eight reptiles complete their dimensional portal stick and escape to the 1987 universe. Unfortunately, Splinter is captured by Hun and brought before the Shredder to serve as bait in a trap.
Pooh, Ash, their friends and the 2003 Turtles meet the 1987 universe versions of April O'Neil and Splinter, and then return to the 2003 universe with the 1987 Turtles vehicles: the Party Wagon and Turtle Blimp. However, they discover that in their absence, the Shredder and the Bowser Family have fused the sciences of the Utroms and Dimension X and rebuilt the Technodrome as a truly terrifying war machine, filled with legions of improved robotic Foot Soldiers and mutated Purple Dragons. During their battle they meet Spider-man, another hero of New York. Entering the fortress to recover Splinter, our heroes and the Turtles are defeated, and Shredder then reveals his master plan: He has discovered while using 1987 Shredder's to survey the multiverse in his plan to conquer it that there are not just the Turtles of the 1987 world and the 2003 world, but scores of them. Knowing that the turtles of those dimensions would stand in his way to conquer those worlds, 2003 Shredder decided to destroy them all by eliminating the original "Prime" universe.
The Shredder scans the eight Turtles, each secured within an enormous spherical centrifuge-like device contained within the Technodrome, to locate the base similarities between them that will pinpoint the location of "Turtle Prime", and the brothers apparently do not survive the process. Once Shredder has teleported the Technodrome away across the dimensions to Turtle Prime, however, Pooh, Ash, their friends and the Turtles reappear, having been saved from oblivion and prisonment by Karai and the Bowser Family, who have realized The Shredder's mad ambition would also spell their own destruction.
With their world being erased around them as the Shredder's plan goes into motion, the heroes and the Turtles break into Purple Dragon headquarters again to appropriate some of the tech the criminals stole, in order to upgrade their dimensional portal stick and follow the Shredder to Turtle Prime. They're attacked by Hun again, who's still seeking revenge for his mutation. However, when he sees what's happening to the world, Hun surrenders the tech just before he's erased. The heroes and the Turtles accomplish their task, and are whisked away to the grim, gritty and monochrome world from whence all Turtle realities sprang. They are attacked by the native 1984 "Prime Turtles", but they eventually manage to convince their ferocious progenitors to help them save all of creation.
Our heroes and the twelve Turtles, with the aid of Splinter, Karai, the Bowser Family and even the 1987 Shredder and Krang, engage the Shredder in battle, but he grows to massive height using molecular amplification technology from Dimension X and seems impervious to their attacks. When the Shredder is accidentally clipped by the energy beam from the Technodrome, however, his armor is damaged, and both heroes and villians try to force him into the beam ... before it is abruptly cut off when Bebop and Rocksteady trip over the power cable and unplug it. The Shredder takes this opportunity to grab the 1984 Turtles and begins crushing them. The world begins to fade just as the 2003 world did, but Shredder hesitates when he notices that he too is fading. Karai attempts to appeal to her father, telling him that what he's trying to do will destroy them all, including him. But the Shredder has become too obsessed with revenge and decides he doesn't care, and resumes his assault. At the last minute the 1987 Turtles throw explosive throwing stars at him, causing him to trip and drop the 1984 Turtles. Shredder resumes his attack - until Bebop and Rocksteady plug the beam power cable back in and thus inadvertently obliterate the Shredder.
With their foe defeated, Pooh, Ash, their friends and the Turtles watch as their respective realities restore themselves. The Bowser Family take the Technodrome as their own and return the 1987 characters to their homeworld, while the our heroes and 2003 characters use the portal stick to return to theirs. The 1984 Turtles decide to go get some pizza to eat ... as somewhere else, across time and space, Peter Laird and Kevin Eastman put the finishing touches on the first issue of Eastman and Laird's Teenage Mutant Ninja Turtles, expressing the hope that the book will sell. But Soon Pooh And His Friends Are Going To Recieve A Great Surprise From Their New Ally The Friendly Neighborhood The Amazing Spider-Man.