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.

Miura Kyoji, a dedicated kendo student, discovers that his shisho (master) Tate Masanari is a reincarnated Incan warrior named Yawaru who wishes to destroy the world to purify it. Kyoji himself is the warrior Bilka, who foiled Yawaru's plans in their previous lives. Yawaru gathers other awakened spirits to release the powers of nature. Now Kyoji must wrestle with his own fate and decide if he is merely a vessel for the reincarnated soul or if he is truly Miura Kyoji and which will be better able to save the world and the future as he knows it.

Ashram, desperate to find a home for his people, is tricked into selling his soul. 300 years later, Pirotesse's devotion to her king remains unshaken. In the sacred world of Crystania, amidst a civil war waged by shape-changing warriors, she searches for her beloved Ashram. She meets Redon, a young prince obsessed with avenging his murdered parents. Together, they confront Ashram's captor -- the bloodthirsty Barbas, who aspires to rule Crystania as "The God's King".

Kasahara Iku and Dojo Atsushi receive an emergency recall in the middle of their date as Japan is rocked by a terror attack. Their new duty is a protection detail assigned to Touma Kurato, an author. Meanwhile, the relationship between Librarians and the Media Purity Committee is also worsening.