The player chooses one character from 4 available: Mega Man, Proto Man, Bass (all from the previous game) and Duo. Each character has different attributes and abilities. Gameplay is almost identical to previous game, "fighting game with gun instead a punches". Game is "boss rush" - player fights against bosses from "normal" Mega Man games. He can use a arm cannon (and Duo's mechanical arm) to attack, and charge them to stronger shoot. After defeating the enemy, the character can take his special skill.
Game has 3 stories (each with different characters): finding Dr. Wily, saving Roll, and recovering the stolen parts.