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The comic tells the story of Captain EO and the ragtag crew of his spaceship on a mission to deliver a gift to a wicked alien queen, the Supreme Leader, on her home world of rotting, twisted metal and steaming vents. Captain EO's alien crew consists of his small flying sidekick Fuzzbucket, the double-headed navigator and pilot Idee and Odee, robotic security officer Major Domo, a small robot Minor Domo (who fits like a module into Major Domo), and the clumsy elephant-like shipmate Hooter who always manages to blunder the crew's missions.
Upon arriving on the planet, the crew is captured and sentenced to be tortured. Before being sent away, EO tells the Queen that he sees the beauty hidden within her, and that he brings her the key to unlock it: his song.