In Ushinawareta Mirai wo Motomete, Uchihama Academy in the Uchihama area is preparing for one last cultural festival before the old school building is closed. Sou Akiyama and the Astronomy Club are drawn into the unease spreading across campus as reports of ghost sightings, accidents, and a strange sleeping sickness begin to circulate. Amid that tension, Kaori Sasaki confesses her feelings to Sou, only to die later that evening in a tragic road accident. Their friends and fellow club members gather in a local hospital to mourn her—yet Kaori appears at school the following day as if nothing happened, and no one senses anything amiss. The day ends without any further incidents, and the group turns back to its festival plans.
Everything changes when an unnatural earthquake shakes the clubroom. The members split up to investigate, except for Nagisa Hanamiya, who stays behind and sees the odd relic-like cube she has been toying with begin to emit a strange blue light. Elsewhere, Sou discovers an unconscious, naked girl lying in a pool of water; she is soon linked to Yui Furukawa, a quiet transfer student whose sudden appearance sets the gears of fate in motion. As the Astronomy Club moves from ghostly disturbances to clashes between student clubs, the story follows their increasingly bizarre efforts to uncover what binds Kaori's impossible return, the mysteries surrounding the old building, and the arrival of the new transfer student.