Geo Stelar, an introvert who lost his dad to a space mission, bumps into EM-being Omega-Xis (aka Mega). When Mega claims to have information of Geo's father, Geo decides to work with him. Partnering up in a "EM Wave Change", Geo gains amazing power, and takes it upon himself to stop Planet FM from invading Earth, calling himself Mega Man in order to protect his identity.
Much like Battle Network, Geo can roam around 2 worlds: the real world as himself, and the Wave World (replacing the Internet from Battle Network) as Mega Man, wherein he is assaulted by nonstop randomly triggered encounters. This game too revolves around going around, collecting battle-cards (aka chips), making the battle deck, EM Wave battles, as well as solving puzzles and generally having to figure what to do / where to go to proceed the story. Throughout the game, there are secondary missions that you could do if you want to from ordinary citizens, but you can only take one bonus job at a time.
In the EM Wave World battle, battle takes place in a 5x3 grid. The player is shown the view behind Mega Man, and he only can go left and right. However, as compensation, Mega Man has a shield which he could block some attacks, as well as the ability to lock-on, serving as the only method to get close to enemies. As with Battle Network, Mega Man can use the Mega Buster either in rapid fire or with a charged shot. Different buster weapons could be found around the EM Wave World or other locations.
As a response to the Syles, Soul Unisons in Battle Network, Star Force has 3 star force types (Pegasus, Leo and Dragon -- 1 per version) which Mega Man can change to. Each has different attributes, charged attacks, and slightly different abilities. You could share the Star Force Powers if you know another player with a different Type (ie. You have Pegasus, they have Dragon or Leo.). However, if you are hit with an attack which has a superior attribute while you are using your Star Force Powers (a water attack on Leo, electric attack on Pegasus and a fire attack on Dragon), then you would take double the damage and revert back to the original Mega Man.
There's a cipher mail system, which you need to type "Cipher" along with a code. The codes are hidden throughout the environments, but are rare. If you find a code and input it, you might be rewarded with different items.
And finally, there's the new Brother Band system. Throughout the game, Geo will become brothers with different characters. The brothers increase Geo's attributes (ie. HP capacity) and the bonuses increase if Geo's level increase (that is, every time Geo buys/finds HP memories). In addition, Geo could also use the favourite cards of his Brothers, although which card you are dealt is selected at random.