A traveler from outside Gensoukyou finds themselves stranded in the realm during its latest incident: a sudden proliferation of strange Puppets modeled after every named character in Touhou's history, from Highly Responsive to Prayers through Double Dealing Character. While searching for a way home, the protagonist captures, trains, and battles Puppets across Gensoukyou's iconic locations — the Hakurei Shrine, the Forest of Magic, Youkai Mountain, the Ancient Capital, and beyond. Along the way, they encounter the Puppet Liberation Front, an organization dedicated to freeing Puppets from their trainers and letting them live without human or youkai control.