Kyūsei Kōshu is based on the manga and anime series 3x3 Eyes. It tells the story of a simple Japanese teenager Yakumo, who lives in Tokyo and tries to study at his high school and to earn his living by working as a cross-dressing waiter at the same time. His father was a famous explorer and adventurer, but he died after a mysterious accident during one of his journeys to Tibet. One day, Yakumo meets a girl who calls herself Pai. She tells him that she belongs to an ancient powerful race of immortals, called the sanzhiyan, the three-eyed ones. It appears that Yakumo's father worked together with Pai, and that Pai's biggest wish is to become a normal human again. Since then, Yakumo and Pai work together, but they must be aware of other sanzhiyan - powerful demons with their own evil plans.
The story of the game is based on the following episode: Yakumo receives a message from his friend, the Buddhist monk Naparvha, saying that a curse has fallen upon a village in China. A young girl was killed under mysterious circumstances, and two monks fell asleep and cannot wake up. Yakumo visits the village and begins the investigation, aided by Yue Hua, the sister of the dead girl.
The game is a Japanese-style adventure. The game world is composed of still shots of locations and characters in anime style, and the player interacts with objects and characters by selecting choices from a menu (such as "Look", "Talk", etc.). Cutscenes are presented as animated sequences.