The story begins on the isolated island of Yamijima located a short distance from the shores of Japan. At midnight, on one fateful night 29 years ago, an under water electric cable snaps causing a total blackout on the island. The events of that ill-fated night result in the disappearance of the island's inhabitants, and to this day, the horrifying incident remains shrouded in mystery. The player begins their story in the present day, with an eclectic group of characters finding themselves visiting Yamijima Island, each for very different reasons. The cast ranges from a magazine editor, who comes to report on the island's past; a blind novelist and his faithful dog; a fugitive, and a fortune-teller.
During the passage to the island a raging tempest hits, turning the sea blood red. Mamoru Itsuki, the magazine editor, is caught in the violent winds and becomes easy prey to a mysterious giant.
Found washed up on the shores of Yamijima, Mamoru meets with the young Yuri Kishida, a mysterious girl who is being pursued by the Shibito (The Living Dead). The two characters form an alliance and together, their journey begins.
On route, they soon meet with two Self-Defence Force soldiers who came into trouble during the storm, necessitating an emergency helicopter landing on the island.
Upon their meeting, a siren suddenly sounds, and the red tsunami lures people to the Netherworld.
The Yamibito (People of the Dark) add another deadly presence as the mystery of this ill-fated island unfurls.