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Thunderian Ships are smaller spaceships which accompany the ThunderCats' Royal Flagship wherever it goes. They provide security to the Flagship as it often contains valuable cargo such as the Sword of Omens as well as holding the Royal family of Thundera.
When the Flagship departed from Thundera just before the planet's destruction, it was accompanied by many Thunderian Ships. Unfortunately, an unexpected attack by the Mutants led to the destruction of every single one of the Thunderian Ships. Even though they do carry weapons on board they were no match for the sheer number and maneuverability of the smaller Mutant Ships.