In the aftermath of the events that transpired in Mega Man 5, the Global Robot Alliance was formed. A year later, the "First Annual Robot Tournament" was held and a mysterious man named Dr. X is its sponsor. The robot tournament was held to determine who is the mightiest robot of them all. Robots from all over the world competed for supremacy. All of a sudden, the sponsor, Dr. X reprograms the eight finalists of the tournament - Plant Man, Tomahawk Man, Wind Man, Blizzard Man, Centaur Man, Flame Man, Knight Man and Yamato Man and announces his plans for world domination.
Mega Man is flabbergasted and asks Mr. X - "Why?" He could not fathom why the seemingly benevolent Mr. X would want to take over the world. He was supposed to be this philantrophist that was supposed to usher an age of peace and prodsperity and not usher an age of chaos and destruction.
Whatever the case, it is up to the Blue Bomber to stop Mr. X at all costs.