Throughout the course of the game, Bomberman encounters a band of space pirates. According to the mysterious Sirius, they are bent on destroying his home planet by leeching away its energy and merging it with a mighty weapon, the Omni Cube! They consist of their leader, Altair, his subordinates, Artemis, Orion, and Regulus, and a slew of baddies and villains meant to make Bomberman's life a rough ride. However, thanks to Sirius' lessons, Bomberman makes short work out of them all: Artemis short circuits, Orion makes two vain attempts to stop him, and Regulus is humiliated in combat. With the three subordinates and the four guardians gone, what is there left to stand in Bomb's way?
In the Black fortress, Bomberman barely survives a barrage of military vehicles, a fully-armed battle robot, and the high-caliber security of Altair's tower. Eventually, Bomb encounters Altair himself, who immediately gives our little friend a good fight. Realizing that he is no match, Altair enhances his own abilities with those of his worker droid, and becomes nearly invincible. Fortunately, a few well-timed bombs save the day! Unfortunately for Bomb, the war is still not over.
When it seems like everything is done and over, Regulus re-appears to save his lost lord. Unfortunately for him, Sirius also joins this "family gathering," steals the Omni Cube, and blasts Altair with its enormous energy. In a last-ditch effort, Bomberman and Regulus mount separate attacks against the traitor, Sirius, and his Rainbow Palace. Bomberman challenges the combined might of Sirius and the Omni Cube, but is overwhelmed. However, just when all seems lost, Regulus comes, once again, out of nowhere and destroys the Omni Cube. Despite this loss, Sirius is still considerably powerful, so Bomberman and Regulus form a temporary alliance against him, and find themselves victorious. They escape from the Rainbow Palace, watch collapse onto Altair's lair, and blow up. Regulus tells Bomberman that he has a newfound respect for his abilities, but still dislikes him. They leave each other's company as rivals... The battle for Planet Bomber is over!