The Mutants set a trap for the ThunderCats by first ambushing and stealing from a Tabbut. The cries of help from the Tabbut attractCheetara and Tygra, just as the Mutants anticipated. As soon as the ThunderCats arrive at the scene, Monkian drops a sticky net on them and traps them. Inside the Cats Lair, the Sword of Omens warns Lion-O and he and Panthro set out in the ThunderTank to rescue their fellow Cats. Panthro maneuvers the tank's jaws to free Cheetara and Tygra from the net. The ThunderCats then turn their attention to the Mutants who quickly flee from the scene.
Inside Castle Plun-Darr, the Mutants are upset that they get constantly defeated by the ThunderCats. They concur that the reason for this is that while the ThunderCats were able to salvage most of their technology, the Mutants' technology lies buried beneath the Desert of Sinking Sands thanks to Mumm-Ra. They go to the Black Pyramid and eventually manage to convince Mumm-Ra to raise their spaceship. From the raised Mutant Mothership, the Mutants gather their equipment as well as SkyCutters and a NoseDiver and transport it all to Castle Plun-Darr.
Armed with new vehicles, the Mutants launch an attack on Cats Lair with Jackalman and Monkian piloting SkyCutters and Slithe driving the NoseDiver. Panthro and Lion-O decide to face the NoseDiver in the ThunderTank, while the rest of the ThunderCats try to attack the SkyCutters using the lair's Laser Beams. Slithe tricks Panthro into following him over a cliff and into the ocean. The NoseDiver, being amphibious, is able to easily navigate through the water but the ThunderTank sinks and gets wedged in an undersea canyon. Using diving equipment from under their seats, Lion-O and Panthro swim out of the tank and try to push the vehicle but Slithe returns on the NoseDiver and starts firing at them. Panthro then sets a trap for Slithe using a nearby cave which is the den of a Giant Eel. As Slithe tries to avoid the eel, the ends up damaging the NoseDiver's energy module causing it to stall.
Panthro and Lion-O swim onto the shore but are immediately greeted by a barrage of fire from the SkyCutters. Lion-O calls the other ThunderCats and he and Panthro head back into the sea to try and free the ThunderTank. Tygra, Cheetara and the Thunderkittens arrive swiftly and dispatch Monkian and Jackalman with ease. Back underwater, Panthro and Lion-O are attacked by a pair of Sea-Quines. Panthro is surprised at the unexpected aggressive behaviour of these normally gently creatures. Lion-O then spots the reason, a baby Sea Quine who is trapped underneath the tank. Panthro and Lion-O try frantically to budge the tank but remain unsuccessful even with the help of the adult Sea Quines. Just then, Slithe returns on the NoseDiver to attack the Cats once again. Lion-O fires a harpoon from the tank and it attaches itself to the NoseDiver which ends up pulling the tank free and releasing the baby Sea Quine. With the NoseDiver damaged, Slithe retreats while Panthro and Lion-O drive the tank onto the shore to meet up with the rest of the ThunderCats.