Following the events of Mountain of Faith, summer arrives in Gensokyo with a fanfare of weird weather. Shortly after the abnormal weather appeared, there was a large earthquake that leveled the Hakurei Shrine, causing Reimu Hakurei to investigate the cause of the incident.

A bizarre phenomenon is occurring in Gensokyo. In the middle of summer, untimely rain and hail fall in the Forest of Magic, snow blankets Hakugyokurou, the Scarlet Devil Mansion is enveloped in a cloudy, dense haze, and the Hakurei Shrine is leveled by a sudden earthquake. Throughout the game, Reimu and the other protagonists set out to investigate the source of the strange occurrences.

Tenshi Hinanawi is a celestial. Finding her newfound life in Heaven boring and monotonous, she enviously saw the youkai of Gensokyo stirring many incidents from above. Wielding the power to control the earth and the divine Sword of Hisou, the jaded celestial decides to instigate a catastrophe of her own.