Gakuen Bomber

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...

[From Moby Games]