During the school's spring break, Kyouya "Kyoro" Shinomiya has once again been kidnapped. Upon release, he finds himself in the GJ Club room, together with his captors, the cute GJ club members. At first glance, Kyoro does not see anything out of the ordinary in the club room, but as he gazes out of the window, he realizes that they are no longer in Japan but in New York!

After the three-pronged conflict between tyrannical electric company Shinra, rebel group Avalanche, and the maniacal Sephiroth, the damaged planet slowly heals its wounds. A rural town dubbed Edge sprouts up on the outskirts of Midgar's ruins. Reeve Tuesti, former Head of Urban Development at Shinra, interviews a young boy named Denzel for potential membership in Reeve's World Regenesis Organization, a group devoted to the restoration and protection of the planet. Denzel recounts his tragic history to Reeve, detailing how the aftermath of the heroic Avalanche's actions laid waste to Midgar and took the lives of everyone the boy knew. Through reminiscing to Reeve, Denzel discovers a newfound purpose.

In the kingdom of Forland, a coup d'etat occurs which leads to the death of the King. In the last moments of his life, the King sends his second child, Princess Alita Forland to escape. Unfortunately, while fleeing, a life and death situation between Alita and the bloodthirsty bounty hunter Falis causes the two of them to switch bodies. Desperate for the safety of her Kingdom, Alita begs Falis to return and protect the Kingdom, offering herself as collateral. After a swift beating on the rebel forces, Falis resumes the title of Princess of Forland, leading to the birth of the most savage princess in their land, the "Murder Princess."

Sometime in the distant future, mankind is forced to live in domed cities while the rest of the world is left to recover from years of environmental hardships. In the Siberian Dome-polis, professional gamer Gainer Sanga and mercenary Gain Bijou commandeer an Overman and lead a mass exodus out of the city.