Intro: Open with Splinter in deep meditation. As we sink into his vision, we see his former master, Hamato Yoshi, standing in front of the Utrom Council of Three, pledging his life to protecting them. Cut to the scene where the Shredder murders Yoshi. We then see the Utrom's planet being attacked by Shredder and his minions. As Splinter’s vision changes, we see Master Yoshi and him standing on a snowy mountain. The pair bow to one another and suddenly Yoshi's Guardian outfit is now on Splinter's body. Splinter arouses from his meditation and states that he understands the message and pledges that he will not fail his master Yoshi, his father.
Act 1: Open in Saki’s mansion where the villain is hosting his own black-tie farewell party. After a short introduction by the city's Mayor, Saki speaks briefly and informs the crowd that Karai will take his place once he departs for home.
Outside, April is trying to gain entry to the proceedings but is thwarted by a guard. Casey arrives dressed like a caterer and pushing a food cart - but the guard blocks his path as well. As Casey and the guard argue, April slips inside. Jones tells the guard to inspect the cart and when he does so, he finds Mike and Raph hiding beneath the table cloth. Mike knocks out the guard and the group heads inside.
Donatello, Leatherhead and Professor Honeycutt (currently stored on Donatello's Tech Tablet) shut down security from an underground access tunnel, allowing Leonardo and Master Splinter to slide down a rope onto the mansion's roof.
On a nearby rooftop, Bishop and his commandos are watching Splinter and Leo as they repel onto Saki's building.
Don, Leatherhead and Honeycutt reach an underground silo after Leatherhead takes out a group of Foot Tech ninjas. Peering into the silo, they see what the Shredder is really up to: a group of Foot Technicians are working on a giant intergalactic spaceship!
Act 2: As the Turtles infiltrate the mansion further, Saki and Karai meet in his inner sanctum. Shredder celebrates his impending journey, relishing in his chance to destroy the Utroms. Karai is saddened by the prospect of his leaving, but he tells her that she will continue to serve him as she always has by running the Foot empire in his absence. The evil overlord then orders her to return to the party and celebrate.
Bishop contacts his spy inside Saki's mansion - none other than Baxter Stockman! Bishop is furious that Stockman didn't inform him about the spacecraft, to which Baxter smugly replies "You didn't ask." Before the discussion can get too heated, Chaplin walks in and Stockman ends the call.
Below ground, Professor Honeycutt cracks into the security system and sets it to lock down. All of the Foot soldiers are trapped in their rooms, including an infuriated Hun, who is in the security room.
Cut to Bishop and his commandoes who are now in the underground access tunnel. Bishop orders his men to seal off the passageway and they begin to rig it with explosives.
Saki is now in his office looking over his spaceship plans. Suddenly, Splinter and Leo enter and attack their arch enemy. Mike and Raph soon arrive and the group begins to battle.
Inside the rocket silo, Don, Honeycutt and Leatherhead have made their way up to a high platform and are looking for a way to get into the control room. Panning down, we see Bishop and his men arrive. Bishop gives the command to blow up the tunnel and dozens of explosions seal off the rocket's launch route. On top of the mansion, the party guests are startled by the sounds of the bombs, but Karai orders an early start to a firework display and everyone is put at ease (for now).
Act 3: Saki continues his fight with Splinter and three of the Turtles. Over an intercom they hear Chaplin cry that Bishop has blown up the access tunnel, trapping the rocket in its silo. Suddenly, Hun enters with a group of ninjas and they attack our heroes. This diversion gives Saki enough time to escape via an elevator. As Saki descends, he orders Chaplin to start the emergency launch sequence (since the access tunnel is now gone). Chaplin worries that there are people on top of the emergency escape hatch, but Shredder doesn't care - with minor reluctance, Chaplin obeys the order and party is seriously over.
On the rooftop courtyard, the floor begins to separate as the silo opens. With the entire courtyard now disappearing, people begin running and screaming, a few unfortunates fall into the silo along with all the tables and chairs. Casey and April save as many folks as they can.
In Saki’s office, Raph, Mike and Splinter beat a path through the Foot and jump down the elevator shaft to the control room below. Hun and his remaining Foot give chase, leaving Leonardo temporarily alone. Karai arrives and pleads with the Turtle to let Saki go - explaining that he will not trouble them anymore if he's gone. Leonardo argues that the villain is leaving to attack the homeworld of the peaceful Utroms. Karai growls that the Utroms are the evil ones for hunting her master and thus deserve their fate, but Leo replies that Shredder has lied to her and he plans to stop him. With that, Leonardo jumps down the elevator shaft.
Down in the Control room, Don and Leatherhead battle the Shredder. Splinter, Mike and Raph arrive to join the fray, as do Hun and his Foot ninjas. Just then, Bishop blasts through a door with his commandos, ordering his minions to kill everyone.
Act 4: As Bishop’s men start blasting, a giant battle ensues. Leonardo arrives with Karai close on his heels. Saki is severely damaged after Leatherhead tears into him. Hun rushes to his master's side and tosses Leatherhead, sending him crashing into a large, chemical-filled tube. Hun lifts Saki and sees that he's some kind of robot - he rips the remaining clothing from the body to reveal that the Shredder is an Utrom in an exo-suit! Hun is stunned and Leatherhead renews his attack. The two giants crash through a window and fall far down into the silo.
Saki recovers and tries to make his way to the ship, but as he crosses a catwalk, Don breaks open a tank of liquid nitrogen that sprays on the evil Utrom. Splinter hooks the exo-skeleton with a chain and pulls it over, breaking it at the ankles and smashing the rest to bits. The villainous Utrom crawls out of the wreckage and is beset by the TMNT and Splinter.
Before our heroes can act, Karai leaps in front of them and grabs Utrom Saki. Karai runs off carrying her master into the ship. The craft's hatch closes before the Turtles get to it. Luckily, Tech Tablet Honeycutt can link to the ship and open the door.
As this is happening, Bishop orders his men to prevent the ship from leaving. Helicopters swoop in and fire missiles into the silo. The rockets hit the catwalk that the Turtles are on just as Honeycutt gets the hatch open. The bridge is blown into pieces, leaving Splinter, Leo, Mike and Raph on one side and Donatello clinging to the opening of the spacecraft on the other. The ship begins to take off - Splinter and the other Turtles have to jump for it!