Amidst a future war between the human race and the forces of artificial intelligence, Joshua, a hardened ex-special forces agent grieving the disappearance of his wife, is recruited to hunt down and kill the Creator, the elusive architect of advanced AIwho has developed a mysterious weapon with the power to end the war and mankind itself. Joshua and his team of elite operatives journey across enemy lines, into the dark heart of AI-occupied territory...

Having sent the evil Dr. Wily scrambling yet again, Mega Man joins Dr. Light and others for an advanced robotics convention. Up for debate: in the development of future robots, should human-like artificial intelligence be pursued or prevented? The event is interrupted when a human extremist group takes over, with the intent of destroying the robots present.