Intro: Hun narrates as he races along the city streets on the Shell Cycle, explaining how Oroku Saki has given him one last chance to prove his mettle.
Act 1: Open with Karai infiltrating a high security warehouse. She sneaks through various obstacles using high tech gadgets to counter the equally advanced security. Karai uses a gas grenade to defeat a group of Bishop’s guards. Finally, the ninja makes it into a vault containing a computer chip, but when she attempts to grab the component, an alarm goes off. Karai escapes the vault's defenses, but as she leaps into the main room, Agent Bishop traps her using a deadly force field created with alien technology. Bishop then contacts Oroku Saki and offers him a trade - Karai for all of the alien technology that he's been amassing since the Triceratons left Earth. Bishop gives Saki 45 minutes to comply with his demands, or Karai will be killed.
Cut to Shredder’s headquarters. Hun and Stockman have been reduced to common laborers in Saki's organization. Both are shackled to the floor with electronic harnesses and Hun is busy shoveling coal into a furnace while Stockman mocks his allegiance to Shredder. Unbeknownst to Baxter, Oroku Saki has arrived and is standing right behind him. As Stockman stammers and lies about what he was saying, Saki activates his harness and shocks the mad scientist into silent submission. Saki then releases Hun and offers him one last chance to prove himself. The giant eagerly accepts and is told that he must rescue Karai or pay with his life. Hun isn't happy to be helping Karai, but he is willing to do anything to regain his master's favor, so he agrees to the mission.
Once Saki and Hun have gone, Stockman secretly boots up his computer systems and hacks into the Foot computers to gain access to their communication systems. Stockman then broadcasts a message in Hun's voice on a channel that he knows the Turtles will receive. Baxter hopes that the TMNT will investigate and ruin Hun's mission.
Inside the Battle Shell, we see the Turtles jamming to some tunes as they drive through the streets. Stockman connects to their radio frequency and delivers his false message. Baxter makes up a story about how Hun is off to capture Splinter and the Turtles. The mutants figure that it's a trap, but they decide to investigate anyway.
Act 2: Hun arrives at Bishop's base inside an armored assault vehicle. The man-mountain pilots the vehicle straight through the walls of the facility, destroying everything that gets in his way, until he reaches Bishop's inner sanctum. Outside, the Battle Shell arrives and the Turtles follow the path of destruction.
Bishop uses a hidden floor elevator to escape Hun's assault. Hun emerges from his vehicle and attempts to pry open the floor to follow his quarry, just as the Turtles arrive. Hun sneers that he doesn't have time for them and tosses a huge canister at the ninjas. The giant then pries open the door in the floor and slips inside. Mikey notes that for a guy that's trying to capture them, Hun sure is being elusive.
Hun reaches the bottom of a stairwell only to see Bishop's private armored subway train pulling away. Hun tosses a tracking device onto the vehicle as it opens fire on him. The Purple Dragon dodges the initial attack, but the train car then launches a huge missile at him. Hun runs for cover as the projectile explodes, ripping the entire base to shreds.
Act 3: On the surface, the Turtles are sprawled amidst the ruins of the building. Hun emerges from the wreckage and heads for his vehicle, only to find it destroyed. The huge man grabs a duffle bag from the wreck and approaches the Battle Shell, ripping open the back door to reveal the Shell Cycle. Hun notes that maybe the Turtles aren't totally useless and he steals the bike and races off, using a wrist comm to track Bishop. The Turtles recover their wits and head for their truck, only to see Hun take off on their motorcycle. Raph is beside himself with anger. The Turtles jump into the Battle Shell and chase Hun.
Back at Shredder’s mansion we see Dr. Chaplin telling Saki that he has set up a monitoring system for all base security and has discovered an unauthorized communication. As Shredder has his aide replay the message, we hear Hun's voice. Saki quickly realizes that Stockman was trying to sabotage the rescue mission.
Cut to New York streets. Hun uses the tracing beacon to find Bishop’s armory, but he is met by one of the agent's security helicopters. The chopper fires on its prey, knocking the man to the ground and destroying the Shell Cycle. Hun then pulls a S.A.M. launcher from his bag and fires it at the helicopter, destroying it.
The Battle Shell arrives and the Turtles pile out. Raph discovers the destroyed Shell Cycle and screams in anger - he then bolts into the armory as Leo tells him to wait for the rest of the team (Raph, of course, does not wait).
Cut back to Hun as he enters an armory. Using a machine gun, he defeats Bishop’s men. As Hun attempts to pry open more elevator doors, Raph enters and attacks. The rest of the Turtles join the fray and again Hun states that he doesn't have time for them. The Dragon manages to elude the Turtles and enters a subway platform where Bishop’s train is. Hun enters the car and finds Karai trapped in an alien prison coil. Bishop attacks from hiding, knocking Hun out of the train. Bishop bids his foe goodbye as the train pulls away from the station.
Act 4: As the train begins to depart, Hun grabs a metal pipe and thrusts it in the track, stalling the train momentarily. Bishop emerges and fires his gun at the giant, who lets go of the pipe and boards the train via another doorway. As Hun battles Bishop, the Turtles climb on top of the train and see both Bishop and Karai - and finally understand what Hun has been up to.
After a protracted battle, Bishop gets the upper hand on Hun and begins to force his head towards the deadly force field encircling Karai. Raph wants to let Bishop and Hun take each other out, but Leo decides they have to save Karai as she had helped them once. Thus the Turtles join the battle and free Karai. With the odds against him, Bishop runs to the front of the train and disconnects the engine from the cars - leaving his enemies behind.
Hun prepares to attack the Turtles in hopes of gaining even more favor from Shredder, but Karai kicks him overboard. The ninja then nods and thanks Leonardo for helping her escape, and then she dives off the train as well. Leo notes that at least she thanked them as the train slowly rolls to a halt. Raph is still distraught over losing the Shell Cycle, but Mikey points out that while they've lost a bike - they've gained a high tech subway car. Don asks Leo if he can keep it, and the leader tells him sure - if he can figure out a way to get it home.
Later, inside Shredder’s mansion, Hun and Karai meet with Saki. Karai thanks her master for sending Hun to save her and then informs him that while she didn't get the computer chip, she did get a scan of it that may suffice in making a prototype. Baxter Stockman enters with two Foot soldiers as escort and thinks he's been summoned to work on the prototype, but Saki angrily informs him that Chaplin will be doing that work - Baxter has been brought here to pay dearly for his betrayal. Stockman begins to scream as the camera pulls away from the building.