The series begins with the destruction of Thundera, and the escape of the central Thundercats characters under the leadership of their wise old leader, Jaga. Jaga doesn't live to see their new home on Third Earth, but he frequently returns as a very Obi-Wan Kenobi-esque shimmering blue ghost. No really specific explanation for the death of Thundera is given in that first episode. It's just a sort of Krypton-esque "we have to evacuate our home planet because it's about to blow up" scenario. It's only much later, in the episode "Thunder Cubs," that we learn the reason for the planet's destruction.

Years earlier, when Jaga was a much younger man, he defeats a mutant leader named Ratilla. Ratilla had carried a double-bladed magical weapon, the Sword of Plun-Darr, an evil equivalent to the Thundercats' own Sword of Omens. Upon defeating Ratilla, Jaga is seen throwing the Sword of Plun-Darr into a volcanic canyon, reassured as it sinks into molten lava that no mutant will wield it again. However, he clearly underestimates the sword's evil magic, and the Sword of Plun-Darr works its way to the core of Thundera, eventually splitting the planet apart.

Thus, the show reveals, although surprisingly little is made of it, the wise adviser who has guided the Thundercats all this time actually made the mistake that cost them everything.