Grey was a Reploid found in a hidden factory in suspended animation, accidentally awakened during battle. Ashe was a human Hunter, chasing after treasures and bounties. After their encounter with the evil Prometheus, they were rescued and taken to a Hunter Base, where their first mission was to help transport a mysterious Biometal. With another attack on the train occurring during their mission, they attempt to protect it - the Biometal, Model A, fuses with them, allowing them to become a powerful Mega Man! But other people are after Model A as well...

Mega Man ZX Advent is the sequel to Mega Man ZX. Players can choose to play as either Grey or Ashe, each with their own storyline and slightly different weaponry, but the overall game remains the same. The game itself plays much like the side-scrolling platformer Mega Man X. However, once the main character fuses with the Biometal, they can transform into Model A, which allows them to steal the data of bosses, taking on their appearance as well as their abilities.