Gunvolt arrives with Mytyl, having rescued her from a mechanical guard, and delivers her to Copen, but Copen's attitude towards Gunvolt is still sour after their prior encounter. Meanwhile, Copen, a human scientist and warrior who harbors a massive hatred of adepts, arrives on the scene to investigate the events, as well as to search for his younger sister, Mytyl, who is hospitalized in the very building the Seraph was about to crash into. Gunvolt races to stop the Seraph from crashing, forced to use his septimal powers as a magnetic cushion to pull the Seraph away from the building, with Joule amplifying her abilities to their limits. The duo make short work of the guards on the Seraph, until they are made aware by Xiao, a young adept whom Gunvolt befriended and acts as his handler on missions, that the Seraph is on a crash course with a skyscraper in the middle of the city. He is accompanied by his girlfriend, Joule, who only exists in the form of Lumen, her own septimal projection known as 'The Muse', as she was physically killed in events prior and bonded herself to Gunvolt's septima. The intruder is none other than Gunvolt, who has long left QUILL behind and works as a solo agent. As the story begins, three executives are aboard the Sumeragi airship, Seraph, arguing about the future of Sumeragi, when an alarm breaks out: an intruder has been cornered. Sometime after the ambitions of Sumeragi Group controlling the whole population of adepts with the failed 'Project Muse' project and the death of their leader, Nova, the Sumeragi Group is in a massive power vacuum. He can also use powers from defeated bosses, similar to the Mega Man franchise. Copen can dash into an enemy and slam into it, which locks onto the enemy and allows Copen to shoot it with targeted attacks. He has an entirely different control scheme, now focusing on his dash attack. The game, however, now adds the option to play as Copen, a character that played a major role in the previous game.

The main character, Gunvolt, controls nearly identically as in the previous game, using a gun to lock onto enemies and then using his electric field in order to attack them. The gameplay is directly based on the one in the original game.

Mighty gunvolt burst unlocks