In the distant future, humanity has found a way to live forever by purchasing mechanical bodies, but this way to immortality is extraordinarily expensive. An impoverished boy, Tetsurou Hoshino, desires to purchase a pass on the Galaxy Express 999—a train that travels throughout the universe—because it is said that at the end of the line, those aboard can obtain a mechanical body for free. When Tetsurou's mother is gunned down by the villainous machine-man hybrid Count Mecha, however, all seems lost. Tetsurou is then saved from certain death by the mysterious Maetel, a tall woman with blonde hair and a striking resemblance to his mother. She gives him a pass to the Galaxy Express under one condition: that they travel together. Thus, Tetsurou begins his journey across the universe to many unique planets and thrilling adventures, in hopes of being able to attain that which he most desires. [Written by MAL Rewrite]

Maetel abandoned her mother and her home planet, the doomed and frozen La Metal, where people must become cyborgs to survive. When she is beckoned to return, her options seem slim: follow her mother's path (and with it a robot mind and the contempt of all humans), or run away and fight with humans against the machines. Yet, she is not without comrades and defenders. If she can accept the friendship of beings of metal who desire peace, and oppose those who think being made of flesh and blood is enough to make one human, she may still have a chance to find her own path. (Source: Anime-Planet)

Despite the destruction of the mechanization home world Andromeda, the machine empire is still swept across the galaxy and Earth has become a battleground. Having returned from his journey aboard the train Galaxy Express 999, Tetsurou Hoshino joins the resistance and fights alongside others who have retained their humanity. When the 999 returns to Earth, Tetsurou receives an enigmatic recorded message from his former traveling companion Maetel, telling him to board the train once more. Fighting his way to Megalopolis station, he makes it onto the train just as it departs. This time, however, Tetsurou is met with several mysteries: Maetel is nowhere to be seen, an ominous "Ghost Train" has appeared, and the ultimate destination of the 999 is unknown. Amid all this, Tetsurou finds himself confronted by the mysterious black knight Faust and soon discovers the machine empire's darkest secret. [Written by MAL Rewrite]

A remake of episodes 51-52 of the TV version.