Adieu Galaxy Express 999 was a sequel to the movie version, which was released in 1981. Adieu presents an entirely new storyline, one taking place two years after the destruction of Andromeda. The machine empire now has even more of a stranglehold over the Galaxy. Rumors are afoot of Maetel being the new Prometheum. Tetsuro, a freedom fighter is shocked when a messenger brings him news - that the 999 is returning. Tetsuro narrowly makes his way to the 999 and departs Earth, now a battlefield.
Although Tetsuro finds that Maetel isn't present on the 999, he does meet Metalmena, a machine woman who has replaced Claire. Also, a mysterious Ghost Train has been travelling the universe and nearly crashes into the 999. The 999 (which now has its own mind) then pouts that it never got overtaken by the Ghost Train. The 999 heads to the planet La Metal, which was actually the birthplace of Prometheum and Maetel. Here Tetsuro helps in the resistance, befriending a man named Meowdar. As the 999 departs, Maetel finally makes her appearance.
Shortly after leaving La Metal the 999 is encountered forced to dock at a station where Tetsuro meets the mysterious Faust. When Tetsuro attacks him, Faust causes Tetsuro to drop into a flashback where he must relive his mother's death. The 999 continues on to the planet Mosaic, the last stop before Great Andromeda, capital of the mechanized empire. Here Tetsuro finds the Ghost Train and is nearly killed.
The 999 finally makes its way to Great Andromeda where Faust greets Tetsuro once more. Maetel meanwhile travels down to the center of the planet where Prometheum's spirit still exists. Maetel is put in charge of the mechanized empire, just like the rumors said, and she reveals the horrible truth to Tetsuro and the others, that the energy the machine people use is actually drained from living human beings. Tetsuro is shocked to find his old friend Meowdar among the dead.
About this time a great comet, Siren the Witch approaches Great Andromeda, sucking up all machine energy. With Great Andromeda collapsing, the 999 is set to depart, but Tetsuro must face Faust one last time. After dealing Faust a fatal blow, it is revealed to Tetsuro that Faust is actually Tetsuro's father. The 999 heads back to La Metal where Maetel and Tetsuro separate once more.