An edited version of the movie was released on July 11, 2009 worldwide on TV. The film was then released on July 29, 2009 in New Zealand, Australia and Canada. In other countries, the film aired on The CW as part of their Saturday morning The CW4Kids lineup on November 21, as part of a 25th anniversary celebration which featured a top-10 episode countdown preceding the film's television premiere. In the United States, an uncut version aired from October 31 to November 14 in a form where three weekly 26 minute episodes were shown in a half-hour slot per week.
The uncut version of the film later appeared on the CW4Kids's website on November 16, which includes 8 minutes of footage cut from the original version that aired on TV. The edited version was released on non-anamorphic widescreen DVD on November 21, 2009 from Nickelodeon/Paramount Pictures home entertainment. The uncut anamorphic widescreen version was later released in 2011 on DVD in the PAL DVD regions (2 and 4). There are currently no plans for an American release of the uncut anamorphic version on home media. On August 24, 2010, Nickelodeon aired the movie on its channel for the first time, then aired it again on August 29, 2010.
The Ninja Turtles are alerted by their master Splinter that they have been careless and discovered fighting the Purple Dragons on TV. Denying this, they set out to break into the Purple Dragons' HQ to get to the bottom of these doppelgängers. Upon doing so, the Turtles discover that their "imposters" are from the 1987 series. They escape together, but the 2003 Turtles find the 1987 team childish as they refuse talk until lunch. They enter a pizza place, only to terrify the citizens, who call the cops; the turtles flee, only for the 2003 Turtles and Splinter to capture them. 1987 Leonardo explains his team was fighting Shredder over Mutagen in the Technodrome; the dimensional teleporter malfunctioned, sending them all to this world. Checking recent tremor reports, the Turtles find the Technodrome; however, 1987 Shredder manages to elude them, forcing his foes to build a portal device to reach their universe for "anti-Technodrome gear". In the meantime, Shredder locates an 2003 Shredder on an icy asteroid. After Ch'rell is thawed out, he is contained for vivisection, as he's too insane to work with; however, his adopted daughter, Karai, breaks into and frees him; she had been monitoring his exile.
While tracking the Technodrome, the Turtles and Splinter are attacked by Hun and the Purple Dragons, who want their mutagen. Although Hun is in possession of a powerful mutant, Splinter destroys it with the Turtle Truck's missiles. Unfortunately, Hun tackles 1987 Donatello into the sewers for the mutagen, becoming exposed; he becomes the very thing he hates - a mutant turtle. He wanders until coming upon the technodrome, now under Ch'rell's control, and vows to serve him again. Ch'rell builds a new exoskeleton for himself, and begins the process of rebuilding the cartoonish fortress into something more worthy of the Shredder; he also improves the Foot bots and mutates the Foot clan. Hun, Bebop and Rocksteady are dispatched to destroy the Turtles, breaking into their lair; it begins crumbling, forcing the Turtles to use their dimensional portal stick to escape into the '87 universe. Splinter is captured by Hun to serve as bait in a trap. Ch'rell uses the dimensional portal, learning there are many parallel universes. He decides to launch an all-out assault on the 2003 universe to lure the Turtles out of hiding.
Back in the '87 universe, the 2003 Turtles meet the 1987 versions of April O'Neil and Splinter. The 2003 Turtles are welcomed as sons and feel a kinship with the 1987 Splinter. After both Donatellos apply their expertise, the Turtles are able to return to the 2003 universe with the anti-technodrome gear and the 1987 Turtles vehicles: the Party Wagon and Turtle Blimp. They find Casey Jones and April attempting to repel the advancing onslaught, and infiltrate the Technodrome, which now looks like the Death Star. Captured by Ch'rell, the Turtles learn they are not the only versions in the multiverse; he plans to kill the "Prime" Turtles, creating a domino effect that erase every other Turtle in the multiverse. All eight are scanned for shared DNA, seemingly vanishing into oblivion as the Technodrome vanishes to the core universe; however, they were teleported them to safety as her father hasn't considered the consequences. Unfortunately, 2003 Shredder has already infiltrated the Turtle Prime universe and is now demolishing it; this causes a chain reaction that begins to literally erase everything and everyone in the 2003 universe, including April and Casey. Needing to upgrade their portal device, the Turtles break into Purple Dragon HQ; Hun is waiting for them, wanting revenge for his mutation. However, when he sees the world vanishing, Hun surrenders the upgrade tech just before he's erased.
The Turtles accomplish their task and just manage to escape being erased, and are teleported to the black-and-white Turtle Prime universe. To their surprise, their originals attack them for no reason, until they mention Shredder. As part of their plan, the other eight will hide while the Prime Turtles lure 2003 Shredder out by insulting his pride. Before he comes out, they are challenged by Shredder Prime, who is comically dispatched by the other hiding Turtles. It turns out Karai has teleported them to safety. With the aid of Splinter, Karai, and even the 1987 Shredder and Krang, all twelve Turtles then engage Ch'rell in battle. 2003 Shredder's exoskeleton grows thanks to molecular amplification technology from Dimension X, but is knocked into the energy the Technodrome is firing and loses some of his suit. Everyone tries knocking him into the beam, but Rocksteady trips and unplugs the power cable. 2003 Shredder begins crushing the Prime Turtles, even though Splinter tells him all of reality, including him will vanish. Too insane to care, 2003 Shredder continues to crush the Turtles until 1987 tosses explosive throwing stars at Ch'rell's leg, causing him to drop the Prime Turtles. Bebop plugs the beam back in, erasing 2003 Shredder from existence.
With their foe defeated, the Turtles watch as their respective realities restore themselves. Splinter and Karai note that Ch'rell always returns no matter how he is defeated, but the various characters decide they'll be there to stop him whenever he may rise again. The 1987 characters take the Technodrome and return to their homeworld, while the 2003 characters use the portal stick to return to theirs. The Prime 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.
None of the original voice cast from the 1987 cartoon series reprised their roles nor was the original soundtrack / score from the show used in this special. In the actors' case, since 4Kids Productions reside in New York City while the majority of the original cast reside in California, hiring them would be expensive and time-consuming as most of them either retired, died or refuse to work on projects unsanctioned by SAG-AFTRA, which was not used in most of their properties. For the score, most of the music from the series is owned by Lionsgate and would require a license fee to be used in the show. For a cost-effective solution, the special used many of the productions' frequent talents and used their in-score team to make a soundtrack that bears a similarity with the original series. The special received negative opinions for the quality of the '87 turtles voices, mostly aimed at Dan Green's portrayal of Leonardo.
Rob Paulsen, voice of Raphael from the original '87 series and voice of Donatello in the Nickelodeon CG series has a huge dislike of the casting direction, as he didn't appreciate Sebastian Arcelus' portrayal of his character, which sounded nearly identical to Paulsen's take.Eric Stuart - Voice Director
The edited version of the movie (which was used for some TV airings and the Region 1 DVD release) removed several additional scenes which remain intact in the "uncut" version of the movie. Some of those key scenes include:1987 and 2003 Donatello work together to locate the Technodrome using underground sonar while riding in their van, which they eventually locate.
2003 Shredder asks to see the trans-dimenstional portal device during his initial tour of the Technodrome.
Karai reveals that she located the Technodrome because her monitoring system for 2003 Shredder had alerted her that he had been transported from his previous location to the Technodrome. She then claims the Technodrome in the name of the 2003 Foot Clan.
1987 Krang and Shredder commiserate about 2003 Shredder ruining their expensive computer equipment in the Technodrome during its renovations.
As part of the renovations to the Technodrome, 2003 Shredder programmed the computer to now utilize all of his extraneous superlatives when it addresses him.
2003 Raphael calls the 1987 Turtles "clowns", which causes an argument. Splinter yells at them to stop bickering and reminds them that they should be working together, causing 2003 Raphael to apologize for the insult.
2003 Casey and April have an extended fight sequence with some enemies who are attacking them.
The 1987 and 2003 Turtles argue about whose Shredder is worse, calling 2003 Shredder "psycho-evil" and 1987 Shredder "decaf".
2003 Leonardo gives a more complete explanation regarding the 2003 Shredder's plan when they initially meet up with the Prime Turtles.
1987 Shredder yells at Rocksteady and Bebop before the Turtles' assault on the Technodrome in Turtle Prime starts.
Karai warns 2003 Shredder that he is making a grave mistake as he attempts to destroy the Turtles, which causes him to pause briefly before being hit by a barrage of exploding throwing stars.