Mega Man Star Force 3 is a unique blend of action and role-playing game (RPG), combining the high intensity combat that is the hallmark of Mega Man games with Star Force's strategic battle system. By defeating enemies and boss characters, players earn "battle cards" that enhance and evolve Mega Man's abilities and attacks.

New to MMSF3 are "Noise Changes," random enhancements that change Mega Man's form and unlock new abilities. The two versions of the game, Black Ace and Red Joker, each have over 100 unique Noise Types that can be combined with Mega Man to unlock elemental powers based on earth, air, water and fire. The new Noise feature will add an exciting randomness to battles, encouraging players to explore, collect and battle across the digital world of MMSF3.

In MMSF3, players will travel between the physical world and the digital world via electromagnetic waves that form "wave roads." Geo Stelar, the protagonist of the game, can see these wave roads through usage of his unique "visualiser" tool. Once in the digital world, Geo can merge with the electronic life-form known as Omega-Xis to become Mega Man. The wave roads are being overrun by mysterious "noise" that change the player's environment and powers in different ways. This noise is being generated by an approaching gigantic meteor that threatens both the physical and digital worlds of MMSF3, forcing Geo Stellar and his crew to fight the oncoming threat to save two worlds. Fortunately, Mega Man discovers that he can control the Noise, using the new "Noise Change" system to transform into many different forms, including the ultimate "Black Ace" or "Red Joker" forms.