The Hakurei Shrine has disappeared. A strange thicket has taken its place, filled with an unnatural magic that is spreading rapidly and bent on disrupting the stability of Gensokyo. With the shrine maiden nowhere to be seen, it's up to ordinary magician Marisa Kirisame to bring back the shrine and its caretaker before it's too late.

Meanwhile in the town of Ponyville, a mysterious shrine has appeared in the Everfree Forest, fiercely protected by an equally mysterious mare. With the rest of Ponyville still shaken by the latest disaster, it's up to aspiring musician Lyra Heartstrings to discover the truth about the shrine and the mysteries within.