A distant planet is collapsing and about to explode. The Thundercats (Thunderian nobles) and the rest of the Thunderian commoners must find a new home just after their home planet, Thundera, explodes. The Thundercats flagship had already safely left and is now travelling in outer space when an enemy known as the Mutants attack and leaves their ship severely crippled. A young boy named Lion-O must learn what it means to become a man and Lord of the ThunderCats as he learns to wield the power of the Sword of Omens.
Accompanied by the Nobles of Thundera, the leader of the ThunderCats Jaga, and his nurse maid, Snarf, Lion-O escapes the the planet's destruction. After acquiring the Sword of Omens, the ship is attacked by mutants from their home world. During the battle, the Mutants try to get onto the ThunderCats' ship to take the Eye of Thundera, a powerful relic that is passed down from generation to generation of leaders of the ThunderCats. Little do the mutants know, the Nobles are willing to die for their leader and the Eye of Thundera.
The Mutants are beaten back, but with a cost to the ThunderCats: Jaga is left to pilot the ship due to a short to the navigation system (autopilot was normally used when flying at lightspeed) while it is in hyperspace. While the rest are in age-slowing sleep chambers , he makes do with what he can, and sets the ship on autopilot when he is no longer able to pilot it. He programs the computers to wake the remaining ThunderCats when they are about to arrive at the planet, and sets the ship on a crash course for the world that will be known as Third Earth.
There again, the ThunderCats must face some of their old enemies, the Mutants, led by Slithe and, due to surprise of all, Lion-O is now a grown-up ThunderCat. His sleep-chamber was damaged and he grew many years older while the others remained in suspended animation. He is now no longer a Thunderkitten and instead, is in an alien adult body like the nobles he must now lead in battle.