Mega Man III uses content from its NES counterpart, Mega Man 3, as well as from Mega Man 4. Following its predecessors for Game Boy, there are only four Robot Masters available to choose at the start of the game, all of which are from Mega Man 3. An additional four Robot Masters are accessible once the first four are completed, the latter all coming from Mega Man 4. Mega Man III also adds some additional features first seen in Mega Man 4, including the ability to charge the Mega Buster to release a charged shot, as well as Eddie appearing in certain stages, dispensing a random aid item.
The game also features a number of changes from its predecessor, Mega Man II: the final four Robot Masters are accessed via a traditional stage select screen, rather than a Wily Teleport System, special weapon energy recharges between the stages of the final four Robot Masters, and Robot Master stages can be accessed again via the stage select menu after the Robot Master has been defeated.
A few months after the events of Mega Man II, Dr. Wily makes a bid for control of the world's off-shore oil platforms. To do so, he stations some of his most powerful Robot Masters that he had ever built at various off-shore locations, and once again, Dr. Light sends Mega Man to investigate and stop them before it gets out of hand. Mega Man takes down the first four Robot Masters and makes his way to the Wily Castle, where he discovers that four more Robot Masters await him. After defeating them, he encounters a new Mega Man Killer named Punk in the Wily Station, whose Screw Crusher delivers a crushing blow to its opponents. However, Mega Man promptly defeats Punk and defeats Wily with Punk's own weapon.