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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.