After the death of his mother at the hands of the evil robot Count Mecha, young Tetsuro has become a delinquent street urchin who dreams only of revenge. Tetsuro lives in a far future world in which humans have the choice to travel to another planet where they can exchange their bodies for immortal, robotic counterparts. His goal is to someday acquire (through theft) enough money to board the Galaxy Express 999, a train which is capable of traveling through space, and which will take him to the planet of robots. One day, after escaping from the police, he meets the beautiful Maetel, who resembles his mother. She offers to take him on the Galaxy Express 999 to get a robotic body and to get revenge on Count Mecha. Along the journey, the two meet many varied people (including Captain Harlock and Queen Emeraldas), and Tetsuro learns what it means to be human.
