A hapless country doctor describes with breathless urgency a night-time summons to attend a young patient. Events soon take on a surreal aspect as "unearthly horses" transport him instantaneously to the bedside. The doctor, preoccupied with personal distractions and grievances against those he is employed to care for, fails to find what is revealed to be a vile, fatal wound. He is humiliated by the villagers, who are "always expecting the impossible from the doctor," and doomed to an endless return trip, losing everything.

Hidden away on a remote mountaintop, the Kokoro Library struggles to attract many visitors. Nevertheless, it is the home of sisters Iina, Aruto, and Kokoro, who consider it their mission to keep the library running in their parents' stead. Kokoro has long dreamed of becoming a librarian at the library with the same name as her, and tries her best to keep up with her older sisters. Due to the lack of patrons, the girls mainly spend their time sipping tea, chatting, and reading. However, as the number of mysterious visitors progressively increases, Kokoro begins to learn about the strange history of Kokoro Library—a place where small miracles seem to blossom.

After a meteor hits Earth, traitor forces have (for all intents and purposes) taken over, and the people are suffering. In the chaos, a boy named Tetsuro Daiba, who had lost his parents in the meteor hit, is paid a visit by Mello, a mysterious woman appearing in a bright light. When Daiba comes to, he finds himself in a spaceship infirmary under observation. Stealing a fighter that he didn't know how to pilot (until he tried it), he breaks out, flying like a total pro. He was able to remember how to pilot from his DNA memory... and to find out more, his doctor friend takes him to his secret underground lab, in which he acts as a professor to find out ways to stop the traitor regime. When the forces invade to take him back, a girl named Rei Yuuki mysteriously shoots down their entire carrier with only a fighter jet! Apparently, both have mysterious powers that the enemies want, which may or may not be connected to their being the only two known survivors of the meteor impact. While looking for a third survivor (which turned out to be a cat), the two are taken by force to Queen Photon (ruler of the traitor regime), who claims that she is out to SAVE the Earth from those who sent the Meteor. The two don't know whether to believe her or Mello until the (telepathic) cat breaks them out of the Queen's sealed chamber, and Mello comes to straighten things out. That's when the two (er, three) of them make a choice... Stay on a planet that can't support their advanced race, or strike out into the unknown of space?

Based on the story by manga master Leiji Matsumoto (The Cockpit, Queen Emeraldas), the 55 minute featurette picks up one year after the events of Galaxy Express 999 in which a young boy named Tetsuro and his motherly companion Maetel worked to rid the universe on the Mechanized Empire who had taken over Earth.