The story of
Mega Man & Bass varies depending on which
player character is chosen. It begins one year after the events of
Mega Man 8 when a
robot villain named
King breaks into
Dr. Wily's laboratory and then the Robot Museum to collect the data blueprints for the creations of
Dr. Light. Dr. Light alerts
Mega Man that he must go to the Robot Museum to confront this new enemy. Meanwhile, Mega Man's rival
Bass hears of the new criminal's appearance and decides to prove himself the stronger robot by defeating King.
Proto Man is the first to arrive at the scene, and King reveals that he desires to create a
utopia in which robots rule the world over humans. King plans to create an unstoppable army using the stolen data, and invites Proto Man to join him. Proto Man refuses and attempts to attack, but King counters and slices his body in half. Proto Man then teleports back to the lab for repairs while King escapes with the data, instructing his minions to handle the heroes. With their own motivations, Mega Man and Bass set out to stop King's plans. After vanquishing eight powerful robots under allegiance to King, the duo infiltrate his castle and engage him in combat. Proto Man interrupts the fight and again attempts to defeat King, but only manages to destroy his
shield, allowing Mega Man and Bass to defeat him in battle afterwards. King questions why they fight so hard for humans when robots are the superior species. The pair explain that humans are the ones who created robots in the first place, which confuses King. The villain reveals that his creator is Dr. Wily, who then appears on a video monitor. When King asks the evil inventor why robots fight each other for the sake of humans, Wily strengthens his "
brainwashing level" and restores his power. Mega Man and Bass engage King in another battle and defeat him. The castle begins a self-destruct sequence and the protagonists escape without King. Mega Man and Bass confront Dr. Wily in his newly regained laboratory. When Wily is beaten, Bass demands to know why Wily deceived him. Wily explains that he created King simply to test Bass' abilities. Wily shows him written plans for making a newer version of King to join with Bass in this venture, promising that the two would be invincible together. Proto Man appears and immediately destroys these plans. Wily then demands Bass to destroy Proto Man, but Bass hesitates. Proto Man tells Bass that although he is a strong robot of free will, he can never defeat his rival because he has nothing for which to fight. Bass dismisses this and forces Proto Man to leave, saying that he will still destroy Mega Man to prove his cause. Meanwhile, Mega Man returns home, but he's sad for not being able to save King. However, his sister
Roll presents him a letter from King, who has somehow escaped the destruction of his castle. King wishes to atone for his own crimes against humans and hopes for them to be friends if they were to meet in the future. ==Gameplay==