Mutilor an evil space pirate tries to steal the world's water supply to sell it to the highest bidder. It is up to the SWAT KATS and Lt. Felina Feral to stop Mutilor and get back the water that he has stolen.
Dark Kat steals super conductive cable from an electrical lab. The SWAT Kats intervene and Razor accidentally blows up a warehouse and injures two workers. Razor feels responsible and leaves T-Bone to fight alone.
When the SWAT Kats, Felina Feral and Ann Gora search for some missing miners in the caverns beneath Megakat City, they soon find the cause of the disappearances: rock scorpions who have been mutated into gigantic, kat-eating monsters.
The SWAT Kats weapons are ineffective against an enormous rock monster that comes out of a demolished sacred stone. They have to find Volcanos weak spot before it attacks Megakat City's Nuclear Power Plant.
When the Metallikats use an experimental tool to repair themselves, their criminal personalities turn it into Zed, a powerful entity that builds an ever-growing armored body around itself and seeks world domination.