Intro: Shredder narrates as we view the recent unfolding of his plans, how he plans to travel through space to conquer the Utroms and the rest of the galaxy. The villain's spaceship is in the silo and begins to launch as the Turtles and Master Splinter jump for an open bay door.
Act 1: Open as Shredder’s ship is taking off. Splinter and three of the Turtles jump and grab onto Donatello's legs (he was already hanging from the open bay door, having been separated from his family by a missile that destroyed the bridge they were all on). The Turtles and Splinter climb their self-made "ladder" and board the vessel. Don pulls himself up with Professor Honeycutt (downloaded onto the brainy Turtle's Tech-Tablet) attached to his belt. As our heroes enter the ship, Chaplin monitors them via the craft's security systems and alerts Shredder (who has been carried inside by Karai and is now being garbed in a new, far more powerful exo-suit) of their presence.
Still on the ground, people are running for their lives as the mansion is destroyed by the launching spacecraft. Leatherhead, April and Casey all get away, as does an angry Bishop. Bishop orders his men to destroy the Shredder's ship with missiles.
As the Turtles, Splinter, and Honeycutt make their way to the ship’s power core, Shredder and Karai prepare for battle. It seems Bishop’s missiles are useless as the ship simply destroys them with lasers upon their approach. However, Baxter Stockman constructed the defense system, and as more missiles, Chaplin is dismayed to discover that Stockman has disabled the security net, allowing the missile barrage to hit the ship. We see Stockman with Bishop - the secret agent is pleased with his new partner's work.
Act 2: As the spacecraft shakes from missile impacts, Chaplin franticly tries to regain control of its defense systems. The Turtles make their way to the ship's power core, where Honeycutt informs them he’ll need time to gain access to the controls. Don plugs the Tech-Tablet into the ship's computer systems and the Professor gets to work. Unfortunately, just as Honeycutt begins, Shredder and Karai arrive.
As the groups battle, it appears that Shredder is unstoppable in his giant new exo-suit. Don and Mike attempt to use some cut power lines to electrocute Shredder, but the villain takes the cables from the Turtles and uses them to defeat Master Splinter. Leonardo and Karai face off; Leo gains the upper hand and she falls over the side of a rail. Leonardo heroically saves her life, but Karai comments that Leonardo is too good for his own good and renews her attack. Leo is thrown towards Shredder, who knocks the mutant backwards into Karai’s sword, impaling him! Leonardo falls to the ground as Raphael cries out.
Act 3: As Shredder turns his attention to the other Turtles, more missiles hit the spaceship. Chaplin can’t gain control of the defense controls, and the hull begins to smolder with fresh missile holes. It seems everyone on board will be cooked as the last two missiles speed towards them. As the torpedoes approach, they run out of fuel and the ship escapes!
Shredder has defeated Splinter and the Turtles and has stopped Honeycutt from hacking into his ship. As the villain is about to finish off Leonardo, Karai intervenes and prevents her master from delivering the finishing blow. The woman states that Shredder has won and asks him to spare the Turtles' lives. Shredder is enraged at her insubordination and he attacks her, sending her flying. Shredder closes in on Karai, but before he can do anything to her, a warhead launched from a nearby satellite hits the ship. The impact from the explosion sends both Shredder and Karai flailing through the entrance and the door slams down, locking them out of the power core room. Shredder orders Chaplin to open the door, and is informed that this will take a few minutes.
The Turtles and Splinter realize that they can’t defeat the Shredder and decide to use their last moments to overload the ships power core and blow it up. Donatello plugs Honeycutt back into the ship's systems, and the Professor dejectedly begins the overload. Chaplin gets the door back open and Shredder runs back inside, but he's too late to prevent the power core from overloading.
Act 4: As the ship begins to explode, time freezes and four Utroms (including Mortu) appear. The Utroms have placed a stasis field around the entire ship, freezing time. The helpful aliens transport everyone off the ship just before the stasis field collapses. With that, Shredder's ship explodes. On Earth, Bishop and Stockman think they have won and the Shredder has been killed.
Later, on the Utrom homeworld inside a courtroom, the Turtles, Splinter, and Honeycutt (in a new body) watch a group of seven Utrom judges. They hear testimony from several alien races regarding the heinous crimes of the Shredder, also known as Ch'rell, Torrinon, Kako Naso, Duke Acureds and Oroku Saki. Upon hearing the testimony, the judges find Shredder guilty of all charges. Shredder is immediately transported to his prison. Karai and Chaplin are sent back to Earth to be handed over to the proper authorities. With that, the Turtles and others are thanked for their help.
Cut to an icy wasteland where the Shredder Utrom stands, crying out in rage and despair. The camera pulls away and we discover that his prison is a frozen asteroid, part of belt that forms an orbiting ring around an alien planet.