Megaman The Wily Wars is a remake of the first three sections of the game, chronicling the adventures of the protagonist, Mega Man. Dr. Wily attempts to vanquish Mega Man by traveling back in time. Wise dispatches formidable robots to dominate the globe. Your objective is to vanquish the nefarious Wily.

Dr. Wily has traveled back in time to attempt to vanquish the robot hero Mega Man in one of their first three encounters. Each game will see Mega Man reliving his previous exploits, with Wily sending out a horde of potent robots to take over the world, which Mega Man must defeat on his own, as in earlier games. Mega Man must use everything he has learned to attack Wily Tower after concluding his time travel.