Dr. Light had an idea: He would build a bunch of good and handy robots to help him and others to make the world a better place. One of these robots is named "Mega" and is designed to help Light around the lab in various tasks. One day, evil Dr. Wily attacks the lab and turn all of the robots evil too. All except Mega. Dr. Light sends Mega to stop these robots and thus, Mega Man is born.

Mega Man: Powered Up is a semi-remake of the original Mega Man. There is an "Old Mode", where one tackles the adventure just like it was in the olden days, with the exception of an added feature to save game. The graphics are souped up, but the level layout is basically the same as in the original with a few minor changes here and there. Then there's the "New Mode" which also features the original level themes and bosses but the levels themselves are boosted with various hidden areas and features which are mostly impossible to get to with Megaman only. The Player must defeat the bosses after which they'll be available as playable characters and use their special abilities to find everything in every level.

The third mode is the Challenge Mode where there is 100 different challenges to tackle and in which one has to dispatch as many enemies as possible in a given amount of time, get to the specific goal in a given amount of time and so on.

In addition to these two main game modes, there is a level editor that can be used to build the Megaman level of one's dreams and play it or send it to the internet where other gamers can download and play it.