Intro: Michelangelo narrates as we see the Triceratons attack Earth and rip Beijing out into the atmosphere. Cut to the Turtles and Fugitoid using the Transmat beam to arrive on Earth. We then see the TMNT breaking Casey and April out of captivity but losing Don in the process. Cut to the Turtles stealing a Triceraton ship and arriving on the Republic Central as a group of Triceraton soldiers surround them in the ship's sewer system.
Act 1: The Turtles are surrounded by a group of Triceratons, who turn out to be Traximus and his rebel army, including the recruits Kluh and Ia from the Battle Nexus tournament. Traximus takes the TMNT to his subterranean rebel base and the group makes their plan for rescuing Donatello.
In the throne room, Don refuses to reveal his knowledge about the Fugitoid's whereabouts. Commander Mozar puts the deadly Triceraton mind probe on Donatello's head and it begins scanning his memories (and frying his brain). Don mentally cries out for Master Splinter. Back on Earth, the Sensei awakes from his meditation and then focuses his efforts to help his son. With Splinter's help, Don is able to block the brain sweep. Zanramon and Mozar are shocked that the terrapin was able to defeat their probe - but the Prime Leader soon comes up with another plan... he'll force Donatello to talk by putting his brothers in mortal peril.
At the United Nations council, we see Zanramon pop up onto the giant video screen yet again. The menacing alien announces that the humans have taken too long to reveal the Fugitoid's location, thus Manhattan is next city to be lifted from the Earth and taken into outer space. A ship hovers over the island city as giant lasers begin carving it away from the land and sea.
Act 2: As Manhattan is being sliced up, Zanramon continues to threaten Donatello.
Back on Earth, Casey and April are traversing the sewers on their way to the Turtles' lair. Unfortunately their path is suddenly cut off as a torrent of water, forced through the sewers by the Triceraton's lasers, barrels down on them. The dynamic duo manage to climb a ladder and escape, but as they reach the streets, they're followed by two mysterious men in black suits, who report to Bishop. Bishop then phones in an angry call to his partner/superior, reporting that it's difficult for him to keep his end of the deal when New York City is being carved up by the Triceratons.
Onboard the Triceraton mother ship, the Turtles, Ia and Monza Ram are making their way through the sewer system. The rescue group enters a security area, defeats the guards and then run a search on the ship's computers for the missing Turtle. The scan reveals that Donatello is being held in Zanramon’s throne room. This is going to be tricky.
Cut to Manhattan as we see another towing device dropped onto the land, which activates an energy dome that surrounds the island and begins to lift it.
In the Triceraton throne room, Don is still being threatened and interrogated by Mozar and Zanramon. The exasperated Turtle asks them is they've tried running a positronic scan of the planet to find the missing robot. Zanramon scoffs at the idea, stating that positronic energy is too plentiful to bother searching for, but Don explains that Earth's technology is too primitive to have any. This news angers Zanramon, who orders Mozar to begin a scan immediately. As the aliens begin their search, Zanramon notes that this had better not be some sort of trick. Suddenly, the door to the room opens and the three other Turtles, who are all bound by handcuffs, are led in by a Triceraton guard with a visor covering his face. The guard reports that the mutants were caught onboard the ship. Zanramon is delighted to have his enemies so close at hand and prepares to shoot them.
Act 3: As Zanramon aims his weapon, the guard suggests that taking the prisoners to the Prime Leader's private torture chamber would be a more pleasing option. Zanramon agrees and the guard takes all four Turtles out of the throne room. As the TMNT are being lead down the corridors, Don states that if this is supposed to be his rescue, it's a pretty lame one. With that, the guard releases the handcuffs, freeing all four ninjas. It turns out that it was all a bluff, and the "guard" is actually Monza Ram. The rescue from the throne room is a success!
Zanramon turns his attention to his vid screen as a groggy Triceraton soldier comes on and informs the leader that the "guard" was an imposter and the Turtles are not actually in captivity. Zanramon orders a full security alert as the TMNT head to a hangar bay to steal a ship and escape. Our heroes encounter resistance, but thanks to Monza Ram they're able to take a familiar ship - Zanramon's cruiser!
Prime Leader Zanramon gets the news and orders the fighter ships be sent in pursuit, but Ia has sabotaged them and they all explode! As the Turtles make their escape from the mother ship, Zanramon orders a fleet of TriBase ships to attack. Several of the giant craft disembark and chase the stolen space cruiser. One of the TriBase ships fires an energy sphere at the TMNT's craft. As the Turtles get closer to Earth, the deployed energy sphere gets closer to them...
Act 4: As Donatello dodges the giant sphere with some fancy flying, two more of the smart missiles are deployed by the other TriBase vessels.
Inside the throne room, the positronic energy scan of Earth is finally complete, proving that the Fugitoid is not on the planet! With this news, Zanramon realizes that his massive attack on Earth was a complete waste of time and resources and his only way to save face is to kill the Turtles.
Donatello pilots the space cruiser down into the Earth's atmosphere and towards the TriBase that's lifting Manhattan. The crafty ninja flies his ship into the Tribase’s docking tunnels with the smart missiles in hot pursuit. The Turtles' craft emerges from the other side of the big ship, but the spheres explode inside the the TriBase, causing tremendous damage that destroys the force field around Manhattan (which slowly drops back into its former setting).
As Zanramon throws a tantrum, Mozar informs him that they have found the Fugitoid's teleportation signal leading away from Earth. Zanramon orders the withdrawal of the entire Triceraton invasion force and the aliens fly off into deep space to find the Fugitoid.
Donatello flies the space cruiser as the Mikey wonders if they should expect a hero's welcome for saving the planet. The exuberant Turtle realizes that they'll have to stay hidden in the sewers instead, but Don remarks that they should look on the bright side - they've now got a cool spaceship and they don't have to worry about the Fugitoid.
With the Earth safe again, a bolt of energy beams into the ground and the Fugitoid emerges in the pit where the TCRI building used to be, wondering if he's arrived too late...