Intro: Splinter recaps the previous episode, ending with the Turtles and him emerging from the Utrom Oracle Pods to face the Shredder and his many minions.
Act 1: Shredder and his minions attack the TMNT and the Utroms. Shredder faces off with Mortu. Leonardo saves an Utrom from an attacking Elite Guard and tosses the alien to Donatello for safe keeping. Mike and Raph are attacked by the Baxter spider 'bot - which packs quite a punch! Shredder gets angry when he sees Stockman fighting and orders him to implement phase four of their plan - Baxter refuses and continues firing at the Turtles, until Shredder activates Baxter's safeguard system which electrocutes the evil brainiac. Forced into painful submission, Baxter heads off towards the Utrom's Transmat. Mortu and the other Utroms rush out to stop Stockman while the Turtles prepare to battle Shredder and his crew. Shredder has other plans and uses a nearby control panel to explode pods and call a portal to the room, which he and his cronies use to escape. The Turtles are trapped in the Utrom Pod room, which is quickly flooding with goop!
Act 2: The Turtles discover that the pod chamber is a Techno-Organic room - made of living material! Cutting it is ineffective, as it quickly heals itself, but Donatello comes up with a plan. Our heroes begin to pound on the living walls with a specific rhythm that gives the room indigestion - causing it to hurl the Turtles through the ceiling and to safety.
Outside, the National Guard General renews his attack on the T.C.R.I. building and orders his men inside. The soldiers begin combat with the Utrom's security robots. Inside the Battle Shell, as a tribute/gag for fans of the original cartoon series, April dons a yellow jumpsuit to disguise herself a news reporter. O'Neil hands Casey a video camera so he can pose as her cameraman in order for the pair to gain entry into the Utrom HQ.
Inside the T.C.R.I. facility, Mortu and the other Utroms try to protect the Transmat from Baxter Stockman, but the Shredder and his minions arrive. The Utroms put up a brief fight, but they're no match for the evil Foot Clan and they're quickly rounded up and forced onto the platform of the teleportation machine. Shredder states he will use the Transmat to beam them somewhere nasty and kill them all. In the nick of time, the Turtles and Splinter arrive. A fight breaks out and Don gets another plan. The thoughtful ninja sneaks behind the Transmat and asks the Fugitoid if he's programmed to emulate any sound - fortunately the 'bot can do this, so Don tells him to impersonate the Shredder to order Baxter away from the machine. Shredder's control over Stockman is voice activated, so when Fugitoid uses the Shredder's voice, Baxter is compelled to listen. Fugitoid orders Stockman to stop working on the Transmat. Shredder angrily tells Baxter not to listen to the Fugitoid. The Fugitoid then tells Stockman to override all voice-controlled protocol, freeing Baxter from Shredder’s control.
Stockman attacks Shredder, leaping onto his chest and activating deadly energy rays that engulf the pair. The Shredder short circuits and falls - defeated by Baxter Stockman! Hun and the Elite Guard rush to their master's side. Hun lifts Shredder and growls that they'll be back, and then the Foot turn to run off. However, before they flee, a small electronic device slips from Shredder's lifeless fingers. It bounces on the floor a few times and then turns itself on. We see that it's a time bomb of some sorts set to go off in ten minutes. Spidery, red lines of energy begin emanating from it and creeping all over the floor and walls. Don rushes to try to stop it, but Mortu yells to him not to touch it, as it's a techno-organic device that contains a virus that could kill him. The bomb has already infected the Utrom headquarters and Mortu explains that the device will cause the entire building to implode when it goes off!
Act 3: April and Casey try to get info from the General, but he angrily orders them away. The Turtles radio April and Casey and inform them that the building must be evacuated - it's going to disintegrate in six minutes! April informs the commander that she's been informed that a terrorist organization has threatened to blow up the building and it must be vacated immediately. The General gets angry again and tells his men to haul the "reporters" away. Inside, the Utroms begin using the Transmat to teleport themselves home and escape the impending implosion. The first pair to beam out features another tribute/gag for fans of the old series - we see two Utroms walking to the Transmat platform, one complains that he hates walking on his tentacles, and the other says, "Shut up, Krang." The pair and a Guardian Transmat out of there.
Outside, a huge beam of energy bursts through the roof of T.C.R.I. headquarters. The National Guard General looks at April and asks how much time he has to evacuate his men. The general gives the order to vacate the premises and the soldiers retreat. On their way out, one grunt gets a shadowy glimpse of a gigantic, reptilian figure making its way deeper into the building.
Back at the Transmat, the Utrom Council prepares to beam out. They are the last group, everyone else has already beamed back home. Mortu invites Fugitoid to return to the Utrom homeworld, and the scientist is overjoyed at the opportunity to live among a technologically advanced and peaceful civilization where his work can be utilized for good. The Fugitoid bids farewell to the Turtles and stands on the platform. Mortu gives Master Splinter a gift - a crystalline ball that the Sensei can use to activate the Utrom's collective memory of their time on Earth, memories that include Splinter's master, Hamato Yoshi. The Sensei focuses for a moment and sees his master training, the two bow to one another and Splinter returns to the present, shedding a grateful tear. Mortu climbs onto the Transmat and Donatello begins punching in the coordinates on the control panel - but just when Don is about to send his friends home, some throwing stars fly through the air and smash into the board, sending sparks flying. Our heroes turn to see that the Shredder has returned with Hun and the Elite Guard!
Act 4: Shredder vows that he will not be denied his revenge after 1,000 years of waiting. The Foot attack, and the Guardians prepare to defend their masters, but Leonardo tells them to stay put and let the Turtles handle this. Shredder attacks, but the combined efforts of the TMNT and Splinter knock the villain back. Hun asks for permission to attack, but Shredder growls that the Turtles are his and orders Hun and the Elite to fetch Stockman, as he can still be useful. Hun and the Elite run off in search for the Baxter robot while Shredder renews hi attack on the Turtles. Donatello now has the opportunity to activate the Transmat, and its beam engulfs the Council, Mortu and the remaining Guardians. Shredder close in effort to prevent their escape, but he's too late and they disappear. Shredder is livid and states that the TMNT have only been a thorn in his side until now, but since they've destroyed his millennium old plan for revenge, he will now kill them! Shredhead attacks and dishes out some punishment to our heroes, but Donatello comes up with yet another plan. He tells his allies to pierce Shredder's armor, and everyone focuses their efforts on that task. Shredder is left standing with numerous weapons stuck into his armor which sparks with escaping energy. The villain initially shrugs off this strategy as a pointless endeavor, but Donatello tells his nemesis not to be so sure. Don then he takes to wires from inside the Transmat and uses them to create a powerful arc of electrical energy that leaps onto the Shredder's armor and electrocutes him! The Shredder falls to the floor, motionless.
The Turtles wonder if they've finally defeated their enemy, but the suit begins to open up - revealing the Utrom inside! As the alien emerges, we see that it's the very same criminal that caused the Utrom's ship to crash on Earth all those centuries ago. Raph laughs at the Shredder Utrom, surmising that he's not so tough without his Exo-suit. This infuriates the alien and it leaps onto Raphael's head, smothering him. Leo tries to free his brother, but the Utrom Shredder snaps at him with vicious, pointy teeth. Splinter comes to the rescue, prying the Utrom off of his son's head with his staff. The evil alien flies across the room and takes cover behind some containers of ooze.
Don has been busy at the controls of the Transmat and calls to his family that it's time to go! The brainy ninja states that he's programmed a better escape route this time, and the TMNT and their master jump onto the Transmat's platform. The Shredder Utrom remembers that the building is about to implode and rushes towards the Transmat in effort to escape. The alien leaps into the air as the Transmat beam begins to teleport the Turtles away - with only seconds to go! The Utrom Shredder lands on the Transmat platform - too late to escape! The implosion device ticks down to one second as the alien's eyes bulge out of its evil head...
Outside, the T.C.R.I. building is swallowed in white light. Casey and April duck behind the Battle Shell, seeking shelter. In a matter of seconds, the entire building has disappeared, leaving behind broken water pipes and a giant crater! April and Casey worry about their friends, just as a beam of energy comes down from space and the Turtles and Splinter fall from the sky, landing heavily on top of the Battle Shell. Don's calculations were a bit too high, but no one is harmed. Casey and April hug their friends and everyone climbs inside the Battle Shell. Police begin to arrive on the scene, so Don fires up the engine. April asks what happened inside and Leo and Don say, "Boy, have we got a story for you..."