Here in the mountains of an eastern land is the comparatively tranquil Hakurei Shrine. The Shrine's only maiden, Reimu, lives here, training to raise her spiritual power, in seclusion within the mountains.

"Training? That's fine and well, but it's time for a good long nap," Reimu says to herself as she trudges up the path back to the shrine. But, upon returning to the Shrine, she finds it overrun with ghost and the like, as something not human has seemingly decided to make it their base.

And so, Reimu took Genjii and, as usual, the Hakurei Shrine's greatest treasure, the Yin-Yang Orbs, and set out to find the source of these troubles and exterminate it. This journey would lead them to strange places, and to encounters with even stranger people...