Intro: Zog narrates as if he is reporting recent events back to the Triceraton Republic. The mighty warrior recaps how his squad had been teleported back to Earth while trying to capture the Fugitoid, and how he was separated from his unit when a firefight broke out in the the Utrom's T.C.R.I. building. The Triceraton explains that he was forced to retreat into the sewers, where he encountered and destroyed "Federation spy-bots" (actually the TMNT's Shell Sleds) and how he attached himself to a Triceraton commando squad (actually Master Splinter and the Turtles) and how "General Splinter" ordered them to "destroy Federation stronghold (actually Shredder's freighter HQ) at all costs."
Act 1: Open with the wharf at night where we see Mike and Zog battling Foot ninjas. Meanwhile, on the bridge of the Shredder's freighter, Raph, Leo and Splinter are battling Hun and four Elite Ninjas. Master Splinter manages to evade the Foot and engage the ship's engines. Donatello is below decks, rigging the wiring to make the ship explode once it's out to sea.
Cut back to Mike and Zog fighting on the pier. The battle goes well for the unlikely duo, but the fight distracted them from being able to untie the last rope moored to the wharf! The freighter pulls out towards the ocean as the rope goes taunt - stopping the ship cold. Everyone on the bridge is thrown to the ground in the lurch, but the battle is quickly resumed. Leo radios Mikey to get the ship untied.
Mikey orders Zog to clear the line and the alien warrior charges rhino-style through a group of Foot soldiers and rips the mooring from the deck with his nose horn - unfortunately the effort causes the Triceraton to lose his balance and he falls into the sea. Mike rushes off to grab the hanging line with several Foot soldiers on his heels. The mutant makes the leap and grabs the lifeline, while his pursuers fall into the drink. Michelangelo hangs on to the rope and then realizes that his ally Zog is missing!
Down in the engine room, Don finishes with the wires and programs the electronic bomb to go off in 30 minutes. As he turns to leave, Donatello is met by four Foot ninjas...
Back on the bridge, Master Splinter is captured and chained by Hun!
Act 2: Hun orders Leo and Raph to drop their weapons or he'll kill Master Splinter. The Sensei tells his sons not to comply, but seeing no alternative, the mutants follow Hun's directive.
In the engine room, Donatello quickly dispatches the four Foot.
Cut to the ship's laboratory, where Shredder forces Baxter Stockman to quickly finish work on the rest of the Foot Mechs. Over the intercom, Hun announces that he has captured Splinter, Leo, and Raph and requests permission to destroy them. Karai protests and states that she promised not to harm them and is honor bound to spare their lives - Shredder states that her duty to him is far more important than her honor. Karai bows her had and stammers that she understands, and then Shredder informs her that her loyalty will be tested - as she will be the one to slay Leo, Raph and Splinter!
Outside, Mike is still hanging onto the cable and calling for Zog, when we see the Triceraton's gloved hand emerge from the depths and grasp the line. Zog begins to climb the rope and reports that his mission is accomplished. Michelangelo is delighted and motions the saurian forward, explaining that they still have work to do.
Cut to the Bridge where Hun and the Elite Guard hold the bound Splinter, Leo and Raph. Karai arrives and locks the door behind her, stating that she wishes the Turtles had not come here, as she must now slay them all. Leonardo sneers, "So much for your word of honor." Karai apologizes, but explains that she must follow her master's orders and draws her blade. Hun grabs Leo's swords and cuts him free, saying that he wants to make things more interesting. Karai and Leonardo fight a close match, Leonardo lecturing his adversary on the meaning of honor.
Eventually Leo knocks the woman to the ground, sheathes his katanas and asks Karai, "Can you live with honor? Show me... here's your chance." Karai grabs her swords and leaps to her feet - Leonardo does nothing to defend himself. The woman strikes at the Turtles' head - but stops the attack inches from his skull. Hun laughs and applauds, happy to see that his rival was unable to fulfill their master's orders. The giant then closes in on Leonardo...
Act 3: Hun is about to finish Leo when Zog, Mike, and Don enter. As the Turtles defeat the rest of the Foot ninjas, Zog throws Hun through a steel door into the ocean. Karai lowers her blades, bows her head and states that she has failed her master. Splinter steps in and tells her that it is alright - she did not do her duty because it went against her honor. Karai looks up with a sorrowful look on her face, and Leonardo smiles at her. Donatello announces that they only have five more minutes until the ship explodes, and the Turtle team heads out, leaving Karai to fend for herself.
The TMNT and others are met by Shredder and a squad of Foot Mechs on the main deck, where another battle ensues. The Foot Gunners prove to be formidable foes for the Turtles with their lasers, buzz saws and chains even though Baxter wasn't able to finish them properly. Splinter faces off with Shredder while Zog destroys the Foot Mech political imposters. Raph grabs the laser-gun arm of one of the Foot Gunners, causing it to shoot wildly - it eventually hits an oil drum, causing a huge explosion and fire!
Act 4: The explosion causes the main deck to collapse, taking everything and everyone with it to the lower level laboratory, where the heroes and villains renew their skirmish. The fight continues as the lab begins to go up in flames. Splinter is injured from the fall and Shredder moves in for the kill, but Zog intervenes and attacks the Foot master. The Triceraton rushes the villain and smashes him with two giant fists, sending the evil leader flying into a hole in the floor that's billowing flames.
Don frees himself from some debris and notes that they only have two and a half minutes before the ship explodes - and then he runs into Baxter Stockman's brain - the mutant is surprised to see the scientist in this state.
Our heroes defeat the remaining Foot Gunners with one minute remaining. The group starts to run for the exit when the Shredder leaps out of the fiery pit and confronts them. Once again Zog attacks and initially defeats villain by smashing him into the floor with a girder. The Triceraton turns his back on his foe to celebrate victory when Shredder leaps up and stabs the alien warrior in the back.
Shredder closes in on Splinter and the Turtles - but Zog stands up and attacks yet again. The Triceraton soldier grips Shredder in a bear hug and carries him back to the pit of flames, asking the Turtles to "tell the others that Zog fought bravely for his comrades, for the Republic, for victory!" and with that the warrior leaps into the inferno, carrying Shredder with him!
Raph wants to try to save Zog - but there's no time. Splinter states that Zog has given them their lives, and they must not dishonor his brave sacrifice - they have to escape! Our heroes dive off the deck mere moments before the freighter blows up and sinks.
Cut to the wharf where the Turtles and Splinter are watching the smoke filter into the skyline. Leonardo states that it was a real honor to have fought alongside Zog, as he was a great warrior. Mikey looks down in anguish.
Later that night we see a helicopter flying low over the ocean. Karai is the pilot and she drops a grapple hook and line, picking up the thought-to-be-dead Shredder. The chopper then flies off into the distance.
Back on the surface of the sea, we see the jar containing Baxter Stockman's brain pop up. "Aha!" the disembodied scientist exclaims, "Once again Baxter Stockman has cheated death!" And with that, the tube sinks back into the ocean.