Intro: Open in the Turtle Lair where Mikey and Raph are fighting over the TV remote. Eventually all four Turtles are battling over the device, but Master Splinter uses his own ninjitsu skills to bind the young ninjas in a carpet. The Sensei grabs the remote and prepares to tune into his favorite soap operas that will begin in five minutes. Mikey states that they still have five minutes to watch his sci-fi show and he reaches out his leg, tapping the remote with his toe. Suddenly the lair is engulfed in blinding blue energy. When the burst of light dissipates, our heroes find themselves without weapons or clothing in a dilapidated, run-down version of the lair. Rushing to the surface, they find themselves not in present-day New York, but in a completely new, futuristic metropolis!
Act 1: As the Turtles and Splinter look around in wonder, they decide to investigate their bewildering new environment. A group of Triceratons pulls up in a delivery truck. Mikey decides to take action. Leaving the others, the rash ninja jumps into the back of the vehicle and, much to his surprise, discovers that the Triceratons are hauling futuristic newspapers! Mike is distracted by the holographic reviews of video games and the door of the truck slams shut, sealing the Turtle inside! The Triceratons take off, unaware of their new passenger. The others chase after the truck by hopping on other cars in hopes of helping Mikey, but as they go higher on the highway, they enter a high gravity zone with poor oxygen. Our heroes gasp for air and fight just to stand in this new sector of the city. Raph manages to leap onto a car that pulls up alongside the delivery truck, but due to the circumstances, he's unable to grab Mike and instead falls onto the street. The Triceraton vehicle zooms off with Mikey still inside as vehicles swerve to miss the rolling turtle. A huge accident ensues. Sirens sound and numerous police vehicles arrive, surrounding our heroes.
A robotic police officer named Constable Biggles emerges and determines that the weakened Turtles and rat must be undocumented aliens. As he turns to inspect and flatter his troops, the TMNT and their Sensei make their escape by climbing down a support beam. Our heroes are now exhausted from their adventure and barely able to move. A large flying limousine arrives and the driver tells the Turtles to get inside if they want to live...
Act 2: Seeing no other alternative, Splinter and his sons climb arduously into the stretch limo, which escapes unnoticed by the pursuing police. Inside the car, Splinter and the Turtles (minus Mikey) are greeted by Serling, the robot driver. Serling gives the Green Team high-tech gear (an Enviro Pack, Graviton Regulator and Wrist Translator) so they can breathe, adjust to different gravities, and translate alien language.
Meanwhile, Mikey accidentally finds his way out of the delivery truck. The Turtle bounces through traffic until he finally falls into a dumpster in a low gravity area.
Cut back to the others as the limo finally arrives at its destination, a luxurious penthouse inside an equally impressive skyscraper. Serling introduces the TMNT to his master, a young male teen. The lad greets the heroes with enthusiasm and shows them his shrine to the Turtles, which contains old newspaper clippings, original Turtle gear, various vehciles, an empty TCRI ooze container, an Utrom exo-skeleton, a dormant Fugitoid, Baxter Stockman's robotic body and Foot Clan paraphernalia that includes Shredder's suit of armor!
The boy stands in front of a podium holding Casey Jones' hockey mask and golf bag and explains that this is his collection, left behind by his great-grandparents, April and Casey Jones! The chipper teen is Cody Jones, the extremely rich owner of O’Neil Tech, and heir to the Jones/O’Neil fortune - and he's accidentally brought the TMNT to New York City in the year 2105!
Act 3: Cody explains that he had read all about the TMNT in April and Casey's journals and he was inspired to create a machine that would allow him to view their exciting past. The young scientist was successful in creating his "time window", but unfortunately it had an adverse side-effect and rather than just allowing Jones to watch the Turtles' exploits, it actually teleported them to the future! Cody reveals that he has no idea why this happened and thus he cannot send them back home. Serling makes Splinter a new outfit while the TMNT don their old masks (taken from Cody's collection).
Cut to Mikey, confused and suffering from the gravity and poor air quality. A phantom-like stranger approaches and motions to the packs that all of the pedestrians are wearing. Mikey figures out that he needs his own gear to get around. The stranger motions for Mike to follow him into an alleyway. Having few alternatives, the ninja struggles to keep up with the stranger as he travels deeper into the darkened alleys.
Back at Cody's apartment, Jones and Don figure out a way to track Mikey. Cody takes the Turtles to a giant hangar and introduces them to the Hovershell, a futuristic vehicle Cody made from one of Don’s future designs! Our heroes pile into the vehicle and take off - as they do, Cody explains that he hasn't had much practice with the Hover Shell - which is very apparent by his poor piloting skills!
Cut to Mikey as he enters the alleyway and approaches a lone vehicle. Hands emerge from the street and grab the Turtle's ankles as a group of men, all dressed the same as the stranger, materialize from thin air. The door opens on the truck and we see a group of aliens imprisoned there - Mike determines that his "friend" is a slave trader. Mikey is now the prisoner of the Street Phantoms!
Act 4: Just as the Street Phantoms are grabbing Mikey, Cody and the others arrive in the Hover Shell. Cody remains on board as Leo, Don, Raph, Splinter and Serling hit the street to save Mikey. A fight ensues. Serling gives Mikey the same gear he gave the others and the jubilant ninja joins his brothers in battle. The combat is particularly difficult because the Phantoms can make themselves as intangible as ghosts. Splinter explains that rather than going on the offensive and literally grasping at thin air, they must go on defense until their foes become corporeal. At that instant, they must attack. Using this tactic, our heroes defeat most of the Phantoms. Their leader, Jammerhead, tries to sneak-attack the Turtles from behind, but Cody spots the villain and smashes into him with some skillful piloting of the Hovershell - apparently the kid is a quick study!
Jammerhead recovers and vows vengeance before disappearing into a wall. Our heroes fly off in the Hover Shell just as officer Biggles and his police force arrives. Upon seeing the unconscious Street Phantom gang, Constable Biggles orders his men to arrest the slave-trading criminals (and takes full credit for capturing them).
Back at the penthouse apartment, Cody worries about the Turtles' ability to adjust to the future. Mikey finds the holographic TV remote and begins to explore his options - until Raph arrives and takes it from him. Splinter smiles, pats Cody on the shoulder and tells the boy that the Turtles will have no trouble adapting to the year 2105.