When 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 dopplegangers, our Turtles discover that their "impostors" are, in fact, versions of them from another dimension. The goofy otherdimensional "1987 Turtles" prove to be a hassle for the more serious-minded "2003 Turtles", 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. 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 the Turtles down. The Technodrome escapes, and the Turtles 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. 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 and Rocksteady, Hun finds and attacks the Turtles lair, but 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.
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 has 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. Entering the fortress to recover Splinter, 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 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, the Turtles reappear, having been saved from oblivion by Karai, who cannot stand by and permit her father's mad ambition.
With their world being erased around them as the Shredder's plan goes into motion, 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. With the aid of a repentant Hun, they 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 "Mirage Turtles", but they eventually manage to convince their ferocious progenitors that they need their help to save all of creation. The twelve Turtles, with the aid of Splinter, Karai, 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 the Turtles all 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 four Mirage Turtles and begins crushing them, but hesitates when he begins to feel himself being disintegrated as well. Karai attempts to appeal to her father, stating that all existence is threatened by his actions, including himself, but the Shredder has become too obsessed with revenge and resumes his assault, poised to destroy the original Turtles and everything that sprang from them...until Bebop and Rocksteady, fearing they will get in trouble, plug the beam back in and inadvertently obliterate the Shredder.
With their foe defeated, the Turtles watch as reality restores itself. The 1987 cast take the Technodrome and return to their homeworld, while the 2003 Turtles use the portal stick to return to theirs. The Mirage Turtles are left to return to their rooftop vigil.
Meanwhile, 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, commenting that they hope the book will sell well.