Five elementary school children are spending their summer break camping at a remote mountain village. While on a hunt for their missing rabbit, Pyon-kichi, they find an injured dog in a field with crop circles. After nursing the dog back to health, they are shocked when he suddenly speaks and introduces himself as Pochi Rickman—an alien researcher who has been on Earth researching its plant life. As thanks for saving his life, Pochi offers to take the children to the moon on a sightseeing trip. When they arrive, the group quickly discovers that the moon hides a vast alien metropolis which they begin to gleefully explore. Unfortunately, after hearing that Pochi was severely injured on his mission, the government of the moon issues a travel sanction on Earth, preventing the children from returning home. Left with no other choice, the group journeys around the galaxy in search of a way to safely return to Earth. Amidst their adventure, they are pursued by aliens affiliated with "The Space Show," the universe's most-watched production shrouded in mystery.

In a futuristic Tokyo, several policewomen fight a monster. One of them, Katsumi Liqueur, remembers where she saw it before... Katsumi Liqueur, an American-born woman of Japanese descent, travels to Tokyo to visit her mother, Fuyuka, who is sick in the hospital. She takes a shortcut through an alley after her taxi gets stuck in traffic, only to encounter a monster and two policewomen fighting it. Later, she meets their chief, Rally Cheyenne, who, it seems, has been expecting her, though Katsumi has never met her before. The policewomen want Katsumi to help them fight the monster, but Katsumi, who does not want to believe in magic, resists.

This sequel to the Silent Mobius The Movie 1 continues the timeline of the flashback section of the first movie (Katsumis initial contact with AMP), using some more ideas and persons from the Manga, and being slightly less incompatible to the Silent Mobius series from 1998.

Thousands of years into the future, mankind has colonized other planets across the galaxy and completely forgotten about Earth. On one part of the galaxy, the female space pirates and their colossal starship Sol Bianca get a surprise when a young girl named Mayo stows away on board the ship. The crew then embarks on a journey to Earth to find the whereabouts of Mayo's parents and discover the secrets of the lost planet.