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The Royal Flagship of the ThunderCats is a massive spacecraft that they used to escape from Thundera. The ship itself is enormous in size. It has chambers for each and every member of the crew. It also has a separate chamber for the Sword of Omens, which is its valuable cargo. The ship is capable of traveling long distances in space over a duration of many years For this reason, the ship holds a number of Suspension Capsules in which the crew can remain in suspended animation until they arrive at their destination. The ship also holds a large supply of space rations for its crew.
When Thundera was on the brink of destruction, Jaga and the other ThunderCats boarded the Flagship to look for another planet to settle in. They took with them valuable Thunderian items such as the Sword of Omens, the Claw Shield, the Time Capsule and the Thunderscope.
During its flight, the ship was accompanied by smaller Thunderian Ships which served to protect the main ship. However, the evil Mutants of Plun-Darr attacked the envoy, destroying all of the side ships and forcefully boarding the Flagship to obtain the Sword of Omens. Fortunately, the ThunderCats, armed with their new weapons by Jaga, were able to defeat the Mutants and send them fleeing back to their Mutant Mothership.
While the Mutants didn't succeed in getting the Eye of Thundera, their attack did manage to severely damage the Flagship's navigation system. For this reason, Panthro was forced to set a course to the nearest inhabitable planet, which happened to be Third Earth. Even so, the planet was light years away and so all the ThunderCats had to live in the Suspension Capsules for the duration of the journey.
Jaga choose not to join them. He knew that even in the Suspension Capsules, some aging does take place and he would not have been able to survive. Also he wanted to manually pilot the Flaghsip for as long as possible due to the damage to the ship's navigation system. He did so for many years and with his final breath, he set the Flagship on autopilot.
As the Flagship entered Third Earth's atmosphere, some of its landing devices malfunctioned and as a result the ship crashed on the planet. This caused the ship's cargo and the Suspension Capsules to be scattered all over the crash site. After the ThunderCats all regained consciousness and fought off another Mutant attack, Panthro salvaged equipment from the Flagship and used it to build the ThunderTank.