New features of gameplay when compared to the original ZX game include a homing shot and the ability to carry weapons without a Live Metal. There are 6 Biometal forms in total with addition of the 8 A-Trans forms. The other four Biometals are Models H, F, L, P, and ZX. A secret A-trans becomes available when the player starts a new game after obtaining all 24 medals (gained by defeating bosses in a specific manner) in one file. This is known as Model a(ncient), and becomes usable once the player uses the item. It allows the player to use the 'classic sprite' Model A that was used in the Model a minigame.
Unlike the previous game, both Grey and Ashe play differently, while in the previous, playing as Vent or Aile was simply gender preference. Each character has a different charge attack for the Biometal transes (Ashe and/or Grey get some extra moves for certain forms, and even Model A plays differently among them). However, the differences are very slight, with both still acting the same, movement wise and damage wise. Both have almost exactly the same storyline (with the exception of the completely different beginning), and both still obtain the same transformations.
- Ashe - along with Grey, she is one of the two main protagonists of the game. Model A assists her in her quest.
- Grey - is a Biomatch for Model A. He discovers that he was made as an alternate body for Albert, who created Model A, also known as Model Albert.
- Atlas - is a Biomatch for Model F after she obtains the Biometal F containing the data of Fefnir. Atlas is one of the four new Mega Men and a boss character.
- Aeolus - behaves in a superior manner to all whom he encounters, and these mannerisms imply that he is a member of some higher tier of society. Has the Biometal H containing the data of Harpuia.
- Thetis - a kind boy that loves swimming and the sealife, but he wants to punish and rid the world of people who dump waste into the sea. He is the chosen one for Model L, the Ice Mega Man. Has the Biometal L containing the data of Leviathan.
- Siarnaq - One of the four new Mega Men, Siarnaq has a cold and robotic and personality. He obtains Biometal P containing the data of Phantom.
- Argoyle and Ugoyle
- Albert - the main antagonist of the game, Albert wants to cleanse the world of its deficiencies by destroying all life on it, in order to restore balance to its imperfect state. He is a smart, calm, and intelligent man, but at the same time, insanely evil. He acts indifferent to his "son" Grey, constantly calling him "defective", while he is more sympathetic towards Ashe, showing her far more respect.
The future ... where science and technology have evolved far beyond our wildest dreams. The long, drawn-out war between the Humans and their mechanical creations, the Reploids, have finally come to an end. The two coexist peacefully in this high-tech world.
The Federation Government, Legion, was established following the war. It was an organization responsible for presenting Humans with cybernetic modifications and assigning artificial life spans into Reploids, blurring the lines between man and machine. The two populations, with their destinies more intertwined than ever before, began to found fledgling nation-states around the world.
A new era of history had begun, and several centuries had passed since the war. Old ruins from the previous age were scattered across the globe and became homes to the feral machines known as Mavericks. However, these dangerous areas were also the final resting places of many powerful lost technologies created as a result of the many years of conflict. One entrepreneur took advantage of this buried treasure of cutting-edge technology and used it as a base for forming one of the world's leading corporations. Soon after, the Hunters, a group of people with dreams of getting rich quick, was formed by the Hunters Guild, to seek out the wealth lying around within the ruins.
The temptation of this technological windfall was too much for some, who refused to join the guild and instead sought out the riches all for themselves. These people were called Raiders. In the great Tech Rush, everyone seemed to forget that this buried technology was designed for one purpose: war.