High schooler Tomoharu Natsume is followed everywhere by Misao, the childhood friend who died in a plane crash he barely survived and who now stands beside him as a ghost. His ordinary life comes apart when a locked trunk is left in his care and Kanade Takatsuki, a girl dressed as a shrine maiden, turns up asking for it, dragging him into a hidden war over giant machines called Asura Machina. A contract binds him as an Asura Cryin', with Misao serving as the Burial Doll his machine runs on, while rival factions close in on what the trunk holds.