Ever 17 is set in Japan, in the underwater marine theme park LeMU, 51 meters below the surface of the artificial island Insel Null. After an incident, almost half of LeMU is flooded, and the path to the surface and the communication lines are cut off, trapping the game's characters inside. In addition, LeMU is under large water pressure, limiting time to find a means of escape to 119 hours.

The player takes the roles of two characters, and sees the story from their respective perspectives: Takeshi Kuranari, a student who visited the park with his friends but got separated from them; and an amnesiac boy who does not remember his own name, and is simply called "the Kid". Among other characters are You Tanaka, a part-time employee at LeMU; Tsugumi Komachi, a woman who is distrustful of the others; Sora Akanegasaki, an artificial intelligence and the computer engineer of LeMU, who is only seen through a projection onto the other characters' eyes; Sara Matsunaga, a second-year student and a hacker; and Coco Yagami, a girl who is stranded on LeMU with her dog Pipi.