Following an earthquake in an unnamed prefecture of Japan, a fault is discovered on Amigara Mountain, very close to the epicenter of the quake. On the slopes of the mountain, two hikers meet; a man named Owaki and a woman named Yoshida. The former assumes that they are both here to see the fault, which has captured the attention of the global press. Following the sound of voices to the fault, the two of them marvel at the strange sight before them: countless human-shaped holes in a rock face exposed by the earthquake.
Scientists examining the holes announce that there is no way to find out how deep into the mountain the holes go. They can, however, determine that the holes are not natural and must have been dug from the inside out. The accumulation of soil over the centuries eventually sealed up the entrances, but they have no way of knowing why the holes were made or who would have the technology to do it, especially since they appear to be thousands of years old.
Owaki is distracted from the speculation when he notices Yoshida looking for something. She explains that she came because she saw something on TV: a hole that she swears was her exact silhouette. Ever since she laid eyes on the hole, she has had a strange feeling that it was meant for her to enter. Owaki is skeptical, but another man called Nakagaki overhears and says that the same thing happened to him. Most of the people who have come to the mountain are looking for their own holes. Nakagaki reveals that he has finally found his own hole, removing his clothes and disappearing into it before Owaki can stop him.
The scientists' equipment can find no trace of Nakagaki. A rescue squad is dispatched, but it has to retreat after getting no more than five meters inside the hole. While camping at the fault overnight, Owaki has a nightmare in which he is Nakagaki, trapped deep inside the mountain and unable to move because the hole has been deformed by the earthquake. When Owaki awakes, Nakagaki still hasn't been found, but Yoshida tells him that she has found her own hole at the foot of the mountain. Despite Owaki's continued skepticism, she insists that it was made for her thousands of years ago, and when she goes inside, she will be trapped just like Nakagaki.
Suddenly, a commotion erupts In front of a news crew reporting on Nakagaki's disappearance: a young man has scaled the wall to one of the holes. He shouts "This is my hole! It was made for me!" and disappears inside. Some other people present at the site then begin climbing into "their" holes as Yoshida says that hers is calling to her and beckoning her inside. Growing increasingly hysterical, she admits that she is afraid that she'll die in there, but feels she has no choice but to go. Owaki blocks up the hole with rocks in an effort to reassure her. That night, they share a tent because Yoshida is too scared to sleep on her own. Owaki comforts her and she tells him how lonely she is. He says that her loneliness made her become attached to the idea of the hole, but now he'll protect her. They kiss.
That night, Owaki has another dream; he is a criminal in the ancient past who has committed a horrific crime. His sentence is to enter a hole in the mountain that was dug out specifically for him, carved in such a way that made it impossible to move anywhere but forward. As he walked through it, his limbs and neck were torturously stretched and distorted, far beyond any normal humans; somehow, he remained alive and in agony.
Owaki wakes to find that Yoshida has unblocked her hole and disappeared into it. As he sits mournfully by the mountain, his flashlight falls from his hands and rolls away; to his horror, it reveals his own hole nearby. He is compelled to take his clothes off and go inside.
Several months later, the scientists are informed of another fault on the other side of the mountain. There are more holes there, but they've been deformed by the quake, being elongated and curved randomly. One worker decides to examine one of the holes and shines his flashlight inside. The scientists see something hideous slowly sliding towards them. It is the body of one of the people who had entered their hole on the other side (Possibly Owaki), horrifically disfigured by the warped tunnel - but still, somehow, alive and coming ever closer...
