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Two years after the events shown in Galaxy Express 999....
The Earth is at war with the Machine Empire. All that is left of humanity are some small bands of rebel holdouts. Tetsuro Hoshino, the boy featured in Galaxy Express 999, is part of one of these small bands. It is a very dark time for humanity.
One night, a courier brings a message to Tetsuro. The message is apparently from Maetel and instructs him to board the 999 once again.
After some trials, Tetsuro manages to board the 999 again. Once on board, Tetsuro discovers that the train is all but empty. The only persons there are The Conductor and Metalmena, a rather cold mechanical girl who has taken the place of Claire.
It seems that the entire galaxy is fighting the Machine Empire and this is made evident at the first stop, the moon La Metal that orbits the planet Heavy Melder. There Tetsuro meets another band of rebels and a young catlike man named Meowdar. He also is told that Maetel has taken over for her mother, the Queen Promethium, as ruler of the Machine Empire. Tetsuro refuses to believe this, however. Even more so, when Maetel shows up and boards the train.
On their way to their second stop, 999 is stopped by Faust, the Black Knight. The Black Knight claims that Queen Promethium is still alive. Everyone escapes and Maetel is rescued by Queen Emeraldas.
The second stop is the planet Mosaic, which is located at the gateway to the Andromeda Galaxy.
The third and final stop is the Great Andromeda planet, the capital of the Machine Empire. There many things happen and many secrets are brought to light.
The space pirate Captain Harlock also puts in an appearance.
adieu Galaxy Express 999 is a bit more serious then the original and not nearly as orchestrated as the original. Nonetheless, it is pretty good. The animation quality is quite a bit better then the original, but in some ways the original story was better.