In this prequel set one year after the fourth World War, cyborg and hacker extraordinaire Motoko Kusanagi from the military's 501st Secret Unit finds herself wrapped up in the investigation of a devastating bombing.

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.