Intro: Open in Sh’Okanabo’s ship, deep inside the Chelsea Chasm. As Sh’Okanabo admires his precious gene-seeds, he walks along a row of cages, all containing pigeons. One of the pigeons is “implanted” with the alien gene-seeds and we watch as the bird is encased in a purple cocoon which then breaks open, revealing a transformed animal that is now a monstrous Kanabo-Drone! Sh’Okanabo is almost ready to put his plan into action, but first, he must do a field test to see if everything is in order. The alien releases the infected pigeon to see how well it can spread the Kanabo virus to the human population of New New York. The bird flies into the city and lands at a hot dog stand, where the customers are Cody, Splinter and the Turtles!
Act 1: Open with the Turtles, Splinter, and Cody chowing down on some hot dogs. As they enjoy their old fashioned dinner, the infected pigeon flies inside and lands on the counter top, spreading purple, Kanabo ooze all over it. The shop owner drives the bird off, but the damage has been done - the goo begins to smother the hot dogs! Our heroes finish their meal and prepare to head home. Mikey decides to grabs one last hot dog for later and lags behind. As Mikey walks home, he can’t resist the temptation, and chomps into the infected hot dog.
Cut to Cody’s Penthouse where the guys are enjoying the belches created by the junk food. Shortly, a zombie-like Mikey arrives and begins acting very strange - first he passes out, then he rushes to the refrigerator and begins eating all of its contents - including the vegetables! His brothers try to help him, but Mikey easily overpowers them and bats them away. Cody injects Mike with a tranquilizer, knocking him unconscious. While Mikey sleeps, the others strap him onto an examination table. Cody runs a bunch of tests and we discover that something is in the Turtle's system causing a new mutation. Suddenly, Mike spews purple vomit all over Leo that absorbs into Leo’s skin! The guys focus their attention back on Mikey as he is engulfed in purple tentacles that form a cocoon around him. Seconds later, the alien covering bursts open and reveals a new, mutated Mikey monster! He’s now a stage one Kanabo Drone!
Act 2: Kanabo Mikey breaks out of his restraints and starts smashing all of the lab equipment. He's super strong and can’t be held down by the others. Mike tears out of the room and smashes through a window. The others jump in the Hovershell to track him. As they follow, Don realizes the slime Mikey’s trailing is infectious.
Suddenly, their attention turns to a crazed Leo whose eyes are now glowing red. Leo then begins smashing around the Hovershell, looking for a way out. He hits the “Shell Release” button and the cockpit disengages from the body aa\nd plummets towards the ground. The ship crashes into the roof of a building and Leo escapes. Raph and Cody (now in his Turtle X armor) follow Mikey while Splinter and Don go after Leo.
Cody and Raph follow Mikey into the hot dog shop. They find a trap door in the floor and investigate. As they slowly walk downstairs, they discover the basement is covered in the purple slime. When they reach the bottom, they realize it’s a nest full of angry, stage one Kanabo Drones!
Act 3: As the group of drones prepare to attack, Cody pushes a shelf onto them to slow them down. He and Raph escape up the stairs and barricade the trap door. Cody has a plan on how to slow or reverse the mutation - he just needs to figure out the proper ratio of light to radiation to expose the mutants to - but he doesn’t have a chance to figure it out as Master Splinter and Donatello enter, both in the initial stage of Kanabo mutation! Don and Splinter start chowing down on food. The other drones break through the basement door and Leo arrives, joining the monster menace. The creatures surround Cody and Raph, but just as the drones are about to attack, they stop and kneel on the ground. Sh’Okanabo arrives and tells Raph and Cody to prepare for their future - a world full of Kanabo Drones!
Sh’Okanabo’s explains via flashback how the Kanabo roam from planet to planet, infecting host bodies and taking over. When that planet is used up, the ship takes off again to find another world to infect. This time, Earth is the target!
Cut back to the present - Raph and Cody decide to get the shell outta there. Cody fires up his rockets and blasts out of the building. Raph follows and they escape inside a hover-truck. However, Cody’s armor was damaged and he’s been infected. It’s all up to Raph now!
Act 4: Cody attacks Raph, causing the hover-truck to crash through a wall into the dawn of a new day. As Kanabo Cody is about to clobber Raph, the sun's rays engulf him - Cody falls to his hands and knees, billowing smoke. The mutation reverts and the boy changes back to his normal self! Cody and Raphael realize that sunlight contains the correct light/radiation ratio to save their friends!
Sh’Okanabo stands in front of his Kanabo army, gloating that the Day of Awakening has begun. Raph and Cody smash through the walls, creating holes for sunlight to enter. They then begin ripping through boarded up windows, lighting up the entire area. Everyone turns back to normal, including Splinter, Don, Leo and Mikey. With no more drones and his great plan ruined, Sh’Okanabo destroys and building's structural supports and flees. The TMNT rescue everyone from the collapsing building. The police begin to arrive, so our heroes beat feet.
Cut to a defeated Sh’Okanabo as he throws a tantrum in his ship. Everything was going perfectly if not for the sun! With that thought, Sh’Okanabo begins to plot a way to overcome the obstacle….