Dr. Wily refuses to accept his previous defeat and turns his ambitions toward a stolen time machine from the Chronos Institute, believing temporal manipulation could reshape history in his favor. When the device proves defective, preventing his immediate escape, Dr. Light arrives to investigate the theft and quickly pieces together Wily's involvement using Rush's keen senses. Suspecting darker purposes behind the villain's interest in time travel, Light summons Mega Man and his canine companion to track down Wily before he can repair the machine and execute whatever catastrophic plan he has devised.