Intro: Narrated by the Shredder. Open with a grim vision of the future, where humans and Utroms are enslaved and armies of mechanical robots enforce martial law. The Shredder appears on giant video screens covering much of the architecture and flying vehicles. The villain declares his domination over the Earth and explains how he will use a giant new Transmat to send his armies to other planets to conquer them all.
Act 1: Open in the Turtle Lair. We see Don talking to April via a computer video link. Suddenly, the ground shakes and Don loses his connection. Ultimate Drako appears with the Time Scepter. The TMNT leap into action as Ultimate Drako raises his scepter. Energy encompasses our heroes and freezes them all in a flash of light.
Fade in from the blinding light as Donatello falls to the floor of the lair. The ninja is now alone, and his home has been destroyed and abandoned. Don is momentarily confused as begins to investigate his surroundings. The brainy Turtle soon realizes that Ultimate Drako must have used the Time Scepter to scatter everyone across different dimensions and eras. Donatello decides to check out the surface, where he discovers that Manhattan has turned it into an industrial nightmare. Suddenly, a helicopter zooms in and shines a spotlight onto the Turtle as armed men jump out of cars and demand that the ninja put up his hands and drop his weapons. Donatello begins to comply, but soon notices that these militaristic cops are wearing the mark of the Shredder!
Act 2: As the Foot Gestapo close in on Donatello with their guns raised, a shadowy figure attacks. The mysterious renegade defeats the Shredder's minions and ushers Don into the shadows. The rescuer turns out to be Mikey, only much older, battle scarred and missing his left arm! We learn that in this reality, Don disappeared thirty years ago, after which the other three Turtles split up. With this, Mikey takes Don to see Splinter.
Donatello and Michelangelo run through the city, which is inundated with Shredder's minions searching for any resistance. Giant video screens cover buildings and blimps, projecting an image of Shredder's face as Karai's voice announces that all must serve her master or face destruction. The brothers escape detection and arrive in the shadows of the overgrown, forest-like wasteland that was once Central Park. As they approach a tombstone, Donatello begins to phase shift, but he doesn't teleport away. Upon seeing Splinter's name on the tombstone, Don falls to his knees. Mike explains that Splinter died helping the three Turtles (before they split up). Donatello is enraged that Shredder has managed to cause so much devastation and tells Mike that they need to reunite all four brothers and defeat the Shredder.
Act 3: Mike leads Don to the underground Resistance Headquarters. As Mikey and Don enter, they are greeted by the Resistance Commander, a rugged and much older April O’Neil. Here we discover that Casey Jones was executed by Shredder. The two Turtles are also greeted by Hun and Baxter Stockman, who are joined together by thick cables that run out of Baxter's jar into Hun's chest. April explains that the Resistance rescued the former Foot members from Shredder five years previous when they were scheduled to be executed. Hun sneers that death would have been preferable to his current status.
Meanwhile, Karai walks into the inner sanctum of Shredder's headquarters and informs her master that Donatello has returned. Shredder greets this news with glee, hoping to destroy yet another enemy.
On the surface above the Resistance Headquarters, we see Leonardo arrive. He's wearing a long black coat and dark sunglasses, his face heavily scarred. Leonardo hears a noise and spins, drawing his sword to face... Raphael. Raph has lost his left eye and is also scarred. The two begin to renew their by now ages-old argument over the death of Master Splinter and prepare to fight - but Donatello arrives and separates them. Raphael is delighted to see his long-lost brother and hugs him. Don convinces his brothers to cease their feud and join him in the effort to defeat the Shredder once and for all.
Cut to Shredder’s palace as Karai informs the Shredder that his new monolithic Transmat is nearly completed. Suddenly, the Turtle Tunneler bursts through the floor and the TMNT leap out, with Don in a robotic exo-skeleton designed by Baxter Stockman. The Shredder emerges from the shadows revealing his new Mega Shredder exo-suit (also designed by Stockman).
Act 4: As Mega Shredder attacks, so does Karai and a group of her Karai 'bots. Hun, with Stockman’s brain attached to him, comes wheeling out of the Tunneler. Baxter protests but is helpless to prevent Hun from asking Shredder to take him back. Shredder simply stomps the two with his giant mechanical foot and then smiles maniacally. Raph, Leo, Mike and April fend off Karai and her 'bots, while Don focuses his attack on Shredder.
Mikey is surrounded by a host of Karai 'bots and is cut down. Leonardo bests Karai in a sword fight, but before he can deal a finishing blow, he has to turn and defend himself against one of the 'bots. While his back is turned, Karai stabs Leonardo. Raphael attacks the woman in a fit of rage, but she easily fends off his assault and deals him a mortal wound. Raphael manages to crawl to Leonardo's body before he too fades away. April arrives with a missile launcher and fires it at Karai, who is caught in the blast and soon dies from the damage that she absorbed.
Donatello screams in rage and attacks the Mega Shredder, but Don's exo-skeleton is no match for the Shredder's suit. The villain easily grapples Donatello, tearing his armor apart. Shredder lifts Don up in front of the Turtle Tunneler’s giant drill and gloats over his victory, but Donatello notes that Shredder always did celebrate too early and explains that the whole battle has been an elaborate trap to get the evil alien into position. Don then pushes a button on his exo-suit and chains fly out of the Turtle Tunneler that enwrap both exo-suits in a death-grip. Donatello escapes from his exo-skeleton (as was his plan all along), but Shredder is helpless. The chains begin to pull the robotic armor towards the now spinning drill, which soon grinds the Shredder into pulp.
With that, Don begins to phase out as April tells him to remember that there's always hope. Donatello blinks out and disappears, April bows her head and thanks him for saving the world. Outside, we see the morning sun dawning on Manhattan, finally free from the Shredder's tyrannical rule.