Set in the year between the events of the first two games, the story revolves around two new characters exclusive to the manga: Tyr and Mizuha, and the mystery of severed Gear parts falling from the sky. Members of the Post War Administration Bureau (P.W.A.B. for short) - the secretive organization responsible for many events in the games - serve as the antagonists of the story. Characters from the games, such as Sol, Ky, Axl, Potemkin and Kliff, also appear, albeit with relatively minor roles.

Set in 2016, it depicts events following Frederick's conversion into a Gear and how he found himself trapped in the Gear Project's research facility.