The Galaxy Federation has defeated the forces of the Orn Empire. But the former allies of Orn have united into a single powerful army known as Vios. The Galaxy Federation attacks their headquarters on the planet Aceria, but loses the battle. They then develop a new fighter spacecraft, the FIRE LEO-04 Rynex, and send a trained pilot to neutralize the Vios.

Quest for the Darkstar (Thunder Force IV in Japan and Europe) is, like its predecessor, a side-scrolling shoot-em-up. The gameplay system is similar to that of the previous game, upgradeable default weapons as well as additional ones that can be collected throughout the stages. Unlike the previous games, the player can choose between four different initial stages. It is possible to control the game's speed by tapping or pressing a correspondent button. Another new addition is a powerful Thunder Sword weapon, which the player acquires halfway through the game.