Gakuen Bomber begins with a dream, more precisely, the dream the protagonist of the game, an ordinary Japanese high-school boy, is having: that of his sister having passionate sex with... a female classmate. Since afterwards he begins to dream about spaceships and aliens, he assumes that dream had nothing to do with reality... or has it? Exploring the high school he attends, the hero makes some startling and not very unpleasant discoveries... Gakuen Bomber is set almost entirely in the high-school, and mostly consists of the protagonist wandering around and triggering event scenes (often of sexual nature) that advance the story. However, the player is given considerable freedom to explore the rather large school compounds, interacting with many on-screen objects in point-and-click fashion.