The game was originally to be called "Lunatic Gunstar" but at the behest of Sega of America, who did not approve of the word "Lunatic", it was changed.
Unlike most games in the genre, the player has a life total calculated in numbers. Therefore, death to a player requires multiple hits but just one death will issue the option to continue or to end the game.
The main highlight of the game are its boss encounters, which often feature large enemies made up of multiple sprites allowing for fluid movement.
Years later, a new menace rises. Smash Daisaku, a vicious dictator found out that the Gunstars knew the location of the Mystical Gems. One day, Smash Daisaku kidnapped the Gunstar twins' older brother Green and used a mind control machine to make Green obey his orders.
With Green's help, Smash Daisaku 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.
Note: The Japanese story below - which takes place on Earth - is considered the proper storyline that sets up the sequel, Gunstar Super Heroes.
The world was nearing its end. An evil organization created the ultimate weapon, Golden Silver, the God of Ruin, to destroy countless cities on Earth from the moon. The Gunstars (Red, Blue, Green, and Yellow) seeing the Earth turn into a living hell before them and fueled by anger, had a showdown with the powerful Golden Silver. At length, after an arduous battle, they defeated the evil God of Ruin. To make sure he was never resurrected, they sealed his body on the moon and took the 4 gems that powered him, and sealed them away in separate places on Earth. The Gunstars, having been pushed to their limits, prayed for a new civilization to arrive, and they began their long sleep. All that is, except for one... Time passed, and a new civilization was built on Earth. A legend was spread across the land. "Revive the God that sleeps on the moon, and he will guide the most righteous people to Utopia." Grey, the commander of the dictatorship calling themselves "Empire", believed in this legend and attempted to carry it out. So he sent people to the moon in a battleship called the "Ark", in order to mine for the 4 gems that would call the God forth. It was then that the leader of the underground mining excursion, Professor Brown, uncovered some capsules, in which the Gunstars were having their long sleep. Once they awakened, they learned of the Empire's plan to revive Golden Silver. Their companion, Green, whom they had remembered being with them until the very last moment, had lost his previous memories and was assisting the Empire in the revival of the God of Ruin. "We won't let such a tragedy happen again! We'll get back the gems and put a stop to the revival of Golden Silver!" Once Professor Brown heard the Gunstars words, he decided to betray the Empire and promised to help the Gunstars in their battle.
Shortly after its original release, Gunstar Heroes made its way to Sega's handheld machine, Game Gear. The port was handled not by Treasure, but by development house M2. As the console's power could not be matched to that of the Mega Drive, the game was significantly scaled down, stripping its multi-player mode, Black's Dice Maze, and several graphic effects. It does, however, add in a few new features such as a jetpack level and the chance to drive one of the walker robots from later in the 16-bit version.
On October 6, 2005, Treasure and Sega released Gunstar Super Heroes, a Gunstar sequel for the Game Boy Advance. The game makes few changes to the gameplay, such as having a fixed weapon selection and the addition of overpowered attacks controlled by the trigger.
On February 23, 2006, Sega released a Treasure-oriented entry in their Sega Ages series for PlayStation 2. Named , it contained Gunstar Heroes prominently (to the extent of it being on the front cover), along with Dynamite Headdy and Alien Soldier. Treasure Box also contains the various versions of these titles (such as Game Gear versions, or versions from different countries), as well as digital manuals and other bonus materials.