While walking to school one morning, Suzume Iwato encountered Souta Munakata, a young man who liked to explore derelict sites. The high‑school girl pointed him toward a nearby ruin, but her curiosity made her decide to visit the place herself.
There she found a solitary door that opened onto a surreal realm—an area she could see and sense but not cross. Near the threshold lay an odd stone; when Suzume lifted it, it transformed into a cat‑like creature and darted away. Terrified, she hurried back to school, unaware that leaving the door ajar would have dire effects.
By releasing the "keystone," the malevolent force from that other world could now slip into Japan and wreak havoc. Determined to undo her mistake, Suzume teamed up with Souta—whose real aim was to stop the spreading evil—to locate and seal every open portal before the nation is consumed. They must read old glyphs to locate the hidden keys within rooms.