Taking place after the destruction of the "God of Ruin" (also known as Golden Silver, the final boss) at the end of Gunstar Heroes, the explosion created four moons orbiting the Earth. However, many years later, the creation of a fifth moon reveals a plan to resurrect the malevolent Empire and Golden Silver once again.

Protagonists Red and Blue, named as such in tribute to the legendary warriors from the original Gunstar Heroes, combat the Empire as part of an organization called "The Third Eye". Together with Yellow, the Gunstars must travel to the moons, stop the resurrected Empire, and recapture the Treasure Gems, four mystical stones with an unknown power that drove the story of the previous game. Super Heroes has different storylines based on what difficulty is chosen and which character the player is playing as.

Most of Gunstar Super Heroes's characters are named after characters from the original Gunstar Heroes, and while many of these new characters bear distinct resemblances to the equivalent characters from the first game, one notable exception is Red, who is female, unlike the original Gunstar Red, who was male.