His destiny has finally arrived as the young Shirou Kamui returns to Tokyo after 6 years. A powerful psychic, Kamui vows to protect the happiness of his childhood friends Fuuma and Kotori, even if it means avoiding them. But fate is cruel, whether or not Kamui wants to be involved; he holds the future of the world in his hands, given the choice of becoming a Dragon of Heaven or a Dragon of Earth. The Seven Seals gather, and so do the Seven Angels; all individuals who have their destiny carved out as one who would battle for the fate of the world. What future will Kamui choose to become reality?

In the great city of Metropolis, severe community structures and prejudice dominate a world where humans and robots live together. Unrest and violence increase with each new day. Searching for the scientist Dr. Laughton, suspected to violate human rights by trading organs, the Japanese detective Shunsaku Ban and his nephew Kenichi arrive at Metropolis. In the scientist's laboratory, Kenichi discovers a girl without any memory of her past life. He decides to help her, so they run away together. His uncle follows him and penetrates the dark secrets of the city to find Duke Red, the man ruling from the shadows. Meanwhile, Kenichi desperately tries to protect the mysterious girl from the people hunting her. However, Duke Red and his adoptive son have their own deep reasons for chasing the girl. These reasons are connected to her true identity and the struggle for the domination of Metropolis...

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.