[4] The game was released with two versions: Black Ace (ブラックエース) and Red Joker (レッドジョーカー).

Field gameplay takes place on isometric maps where Geo can interact with his environment and other NPCs.

Replacing the character's fictional handheld device from the previous game is the Hunter-VG, a sort of personal digital assistant where players can access their Battle Cards, status, emails, and various other features.

Hunter-VG's also house artificial intelligent EM wave beings known as Wizards (the spiritual successors to the Net Navis of Mega Man Battle Network).

The Hunter-VG affects gameplay with various pop-up messages that the player has to physically touch on the bottom screen in order to access.

Key words such as locations and characters are also stored to give casual players background if they didn't play the previous two games.

By transforming into Mega Man, Geo can run across the wave road where viruses can be battled via random encounters.

Mega Man is only able to move left or right while his enemies have a wider range of movement in front of him.

However, Mega Man is given the ability to shield and temporarily jump into the enemies' side of the battlefield to compensate.

The Mega Buster is constantly charging to release a single powerful shot, but the player can hold the button down to fire rapidly.

Although cards normally can only be used once per battle, they are all refreshed afterward, so the player is encouraged to use them as the primary means of combat.

For example, exceeding 50% will allow Mega Man to access the power of one of 10 unique transformations based on FM-ian foes from previous games.

This option becomes available on the Custom Screen, giving Mega Man an exceptionally powerful folder to use for the next three rounds of the battle, as well as transforming into a unique finalized form stronger than any other Noise forms (Black Ace in the Black Ace version and Red Joker in the Red Joker version).

Person match, attacking the other player with an element that they are weak to does not deal double damage.

Like the previous game, Mega Man Star Force 3 is available in two different retail versions: Black Ace and Red Joker.

To make matters worse, some Wizards have lost control and gone on rampages due to overexposure to Noise.

A crime syndicate known as Dealer begins manipulating and collecting the Noise for their leader named Mr. King who poses as a charitable businessman for the public eye.

Dealer's true intentions involve manipulating a powerful mass of Noise called Meteor G that is on a crash-course for Earth, and using it to take the world hostage.

Geo Stelar and Omega-Xis find themselves in the middle of various Dealer attacks and begin thwarting their plans as Mega Man.

A young Satella Police member named A.C. Eos (A.C.E or simply Ace) takes notice and decides to enlist Geo as a commando in the fight against Dealer, especially since Mega Man is able to utilize Noise positively.