Rocksteady and Bebop dump a bottle into the ocean which carried the Nanovampire, a parasitic virus. Splinter opened the bottle and swallowed the virus, forcing the Ninja Turtles to Micro mutate and go inside their master, attempting to kill the virus physically. Krang got wind of this and used a device to shrink Bebop, Rocksteady, and Shredder, so they could Super Mutate without worrying about the ill effect the Turtles' Micro mutation had, which would cause them to grow again once the Super mutation wore off. They then had a Foot Soldier sneak into the lair and deposit them into Splinter while April was out buying some ice for sensei's fever.
They encountered the Turtles inside Splinter's heart, and proceeded to Super mutate and trounce them. However, once their Super mutation time limit wore off, the Turtles figured they could have enough time to return the beating in kind and save Splinter before they needed to escape. The Turtles knocked the Foot Clan out of Splinter's heart and outwards into elsewhere in his body, killed the Nanovampire, and left Splinter's body within three minutes.
Back at the Technodrome, Bebop reveals that Splinter eventually pooped the Foot Clan out.
Shredder, Rocksteady, and Bebop are sent to distract the Turtles and Splinter while Krang works on awakening the evil fairy Dark Mu. They Super mutate and turn on power enhancers that Krang gave them, making them even stronger than the Turtles in their own Super mutant forms. Luckily (sort of) for the Turtles, though, Dark Mu's awakening was preceded by global climate catastrophes and the Foot Clan were swept away by a tidal wave.
Rocksteady, Bebop, and Shredder step out of a portal to Japan and are promptly hit by a bullet train carrying the Turtles, April, and Splinter. April and the Turtles witness the villains flying past the train and the Turtles run to fight them. On top of the train, the Turtles are subdued by Bebop and Rocksteady's laser fire. However, the Turtles are saved by Splinter's old friend Hattori Kinzō and his ninja clan, who throw shuriken at them until they are knocked off of the train.
That night, the three of them wander around in the forest, looking for these new MutaStones, and Shredder gets yelled at over the Comlink by Krang. In the morning, the arrive at Kinzō's shinobi village and attempt to steal the mirror containing the MutaStones. Kinzō attempts to lift the mirror's shrine, and in doing so, causes an explosion that blasts both groups outside and onto the ground, leaving them to witness a massive hidden fortress rising out of the ground, with the mirror balancing on the tail of the roof's shachihoko ornament.
The Foot Clan race to the top of the fortress from the outside walls, with the ninja clan and Ninja Turtles following after. Partway to the top, Leonardo asks Kinzō that since it's a castle, should there not be stairs inside? Kinzō is embarrassed that he didn't realize this, and he tells the Turtles to crawl through a window and use the stairs while he and the other ninja continue as-is.
Despite taking the Turtles taking the stairs halfway, the Foot make it to the top first, followed shortly by the ninja clan. To keep the Foot from getting the mirror, Kinzō and the other ninja fling a bunch of decoy mirrors onto the roof. However, as Shredder points out, now the ninja no longer know which is the real mirror, either, leaving the two clans to search the rooftop in an effort to find it before the other.
The ghost Yukimura points out the real mirror, and Shredder gets to it before Kinzō, and the MutaStones adorn Shredder with a tiger armor, Bebop with a fish armor, and Rocksteady with a snake armor. The Turtles finally make it to the top and the newly empowered Foot absolutely overwhelm them. Krang appears and grabs the mirror, wanting to make a hasty retreat to Dimension X before anything goes wrong. Shredder, however, wants to stay and make use of his new power. A startled Krang is then subdued by the ninja clan, and Kinzō takes the mirror from him, throwing it to the Turtles and allowing them to use the remaining MutaStones and gain mutant armor of their own. The Foot then finally decides to retreat, but not before Shredder steals the mirror back from Kinzō. In an effort to stop him, Leonardo fires a dragon blast from his sword, which clashes with a tiger blast from Shredder's. Shredder begins overpowering him, but then the time limit on the Foot's armor lets up, causing them to lose their power. Leo fires another blast and catches Shredder on fire, allowing him to retrieve the mirror. The Foot cut their losses and leave.