Two years after saving the world from a cataclysmic event, the members of the activist organization Avalanche have gone their separate ways. Tifa Lockhart opens a new bar, and her childhood friend Cloud Strife starts up a motorcycle-based courier service. Although most of their former allies have fallen out of touch, Cloud and Tifa live in fragile peace with their two young wards Marlene and Denzel. Their life together begins to crumble as a contagious plague and overwhelming grief pull Cloud away from his newfound family. While distancing himself through his work, Cloud is attacked by three silver-haired figures in black uniforms who bear a passing resemblance to his bitter rival, Sephiroth. As the antagonistic trio stalks Cloud and brings harm to his loved ones, the former mercenary struggles against his own demons while fighting to protect his family and prevent the will of Sephiroth from returning to the planet.

For years, the Niflheim Empire and the kingdom of Lucis have been at war. The empire, having dominated most of the world of Eos, covets the power of the last known Crystal, which is held in Lucis' capital city, Insomnia. In order to protect his people from these advancing forces, King Regis Lucis Caelum CXIII used the power of the Crystal to surround Insomnia with a magical wall. Along with this barrier, Regis assembled an elite military task force known as the Kingsglaive. By drawing their power from the king, the Kingsglaive protect Lucis' borders from the onslaught of the empire and other forces that would do them harm. One such member of the Kingsglaive is Nyx, a man nicknamed "The Hero" by his fellow warriors due to his arrogance and desire to save everyone. However, his pride gets the better of him, causing him to disobey his captain's orders, resulting in a demotion. Now, Nyx spends his days guarding the city gates, but things begin to change once word gets out that Regis plans to sign a peace treaty with their sworn enemies.