Keio Flying Squadron chronicles the adventures of Rami, the little bunny-suited member of the flying squadron tasked with the protection of the "Special Holy Object". Unfortunately as the game starts the object in question gets stolen by the evil Dr. Pon, and so Rami jumps atop her trusty dragon in pursuit of Dr. Pon.

The game plays as a classic 2D shooter with upgradable weapons and option characters, with a distinct cartoonish and family-friendly design. It features seven levels and three difficulty settings.