Two commandos have a huge stockpile of military hardware at their disposal as they attempt to rescue their kidnapped family. Run through military bases and crawl through tunnels all the while shooting in every direction using rotational joysticks.

Midnight Resistance features play mechanics and controls similar to that of the Contra series, and can be played by up to two players simultaneously. The main distinguishing feature is the inclusion of a rotatable joystick similar to the one used in Ikari Warriors, in addition to the traditional set of shoot and jump buttons, allowing the player to adjust his character's aim in one of eight directions by rotating the joystick clockwise or counter-clockwise. This allows the player to keep their aim in one direction while moving in another, even while crawling or jumping