Tetsurou Hoshino is a young street urchin who desperately wants to replace his human body with an android body, which would grant him immortality and the social freedom the androids have. Normally this is incredibly expensive but it has long been rumored that if you board the Galaxy Express headed for the Andromeda Galaxy, at the end of the line is a planet where they are given out for free.
After seeing his mother murdered by an Android Count, he has no reason to remain on his home planet and nothing to hold him back. Now, not only seeking the android body of his dreams but also a way to avenge his loss, he begins to search for a way to board the train alone.
Then he meets Maetel, a mysterious woman who offers him a ticket aboard the train if he will be her companion for the journey.
Their journey will take them to planet after planet, each strange and new, and each stop along the way being an opportunity for Tetsurou to reflect on being human, human actions, and the prospect of immortality. During their travels Tetsurou and Maetel meet, amongst others, Emeraldas and Harlock.