The Gunstar family has been the protector of the planet Gunstar 9 (G-9) for generations. Professor White Gunstar, in his youth, defeated Golden Silver, a destructive android that traveled millions of miles to suck G-9 dry of all its resources. Professor White was able to extract the four famous Mystical Gems (The robot's power source), and imprisoned the robot on one of G-9's moons.

But now, years later, a new menace has arisen. Colonel Red, a vicious dictator (and a very bad dresser), found out that the Gunstars know the location of the Mystical Gems. One day, The Colonel kidnapped the Gunstar twins' older brother Green and used a mind control machine to make Green obey his orders.

With Green's help, Colonel Red has amassed all four Mystical Gems, has turned Gunstar 9's peaceful worker droids into deadly menaces, and is now preparing to leave for Gunstar 9's moon to reactivate Golden Silver. As one of the Gunstar twins, you must fight your way past Colonel Red's Empire Army and retrieve the Mystical gems, or Golden Silver, the Destructor will rise again and destroy your world! Are you heroic enough for the task?

Gunstar Heroes is considered innovative. It combined a linear, side-scrolling shooter with plot elements, a combo-based weapon system, a dice game, recurring bosses, and combat strategy. It remains one of the most popular games of the 16-bit console, and is often found being traded for relatively high prices. In the console's later years it was re-packed in Sega's Classic Pack along other games such as Alex Kidd in the Enchanted Castle, Altered Beast and Flicky. It can now be played on Nintendo's Virtual Console for the Wii.