A young man named Shounosuke sees a strange dream: a voice talks about mankind and its sins, and a beautiful girl begs him to save her... The next day, when he goes to school, an earthquake occurs, and he is miraculously taken into another world, where he meets the girl from his dreams. She says that girls in different dimensions are in grave danger, and Shounosuke has to save them...

Bomber Quest has elements of both strategy/puzzle game and RPG. Each of the six girls has a different scenario, accessible from the beginning. Each scenario puts the player character into a top-down environment. Shounosuke has to build a maze to access its locations. The maze is built from small pieces taken from Tetris. The player can rotate the pieces and then place them onto the ground. The goal is to build a maze that would cover possibly large ground, gaining access to important locations and items. Visiting uncovered locations in the right order leads to cut scenes, which advance the plot.

Shounosuke will be randomly attacked by enemies during his wanderings through the mazes. The battles are viewed from first-person perspective and are turn-based. Shounosuke can only use physical attacks and items. Defeating enemies brings experience points, leveling Shounosuke up in a standard RPG fashion.

The game features scenes with nudity and sexual content.