The gameplay in this sequel is identical to that of the previous entry: the player navigates the digitized images of the girls over 2D backgrounds in a side-scrolling/third-person perspective manner, searching for clues, triggering scenes, and choosing responses and/or actions when prompted by the narrative.

It consists of six independent scenarios, and the numbering of the scenarios is a continuation from the previous title.

Kyuumei-hen is a direct sequel to the first Twilight Syndrome game, continuing the spooky adventures of the three brave and reckless high-school girls: Yukari, Mika, and Chisato. The first mystery involves a girl named Sakura Himegami, who was killed in an accident many years ago; apparently, her ghost is still around somewhere. The trail leads to an abandoned path in the mountains; Mika decides to venture there, while the other two are going back to school at night, hoping to find more clues.