As Vincent and Yuffie Kisaragi help to evacuate Midgar which is about to be destroyed द्वारा a meteor summoned द्वारा Sephiroth, Vincent finds Hojo, an antagonist from the first game, slumped at the controls of a Mako Cannon. The तोप explodes, destroying Hojo and forcing Vincent to escape. Three years later, Vincent is in the city of Kalm, which is attacked द्वारा mysterious soldiers, who capture some of the citizens and kill the rest. Vincent, with the help of his former comrade Reeve Tuesti and the World Regenesis Organization (WRO), an organization dedicated to helping the planet recover from the events of Final कल्पना VII, fights the soldiers and forces them to retreat.

Reeve discovers that the soldiers were members of Deepground, a military organization made up of super-soldiers from Shinra. While confronting Deepground, Vincent discovers he is one of Deepground's target as he holds the Protomateria, which they want to use to control a mysterious being known as Omega. Vincent also carries inside him genes of Chaos, a beast having an unknown relation with Omega and it was inserted into Vincent's body द्वारा his lover, Lucrecia Crescent, who froze herself several years ago.

Vincent goes to the town of Nibelheim where Lucrecia studied Omega and Chaos in order to find और information of her research. While confronting Vincent, Deepground member Rosso steals his protomateria in order to control Omega. Before finishing Vincent, Rosso is ambushed द्वारा Yuffie who rescues Vincent. As Vincent returns to the WRO, he finds that Deepground has assaulted WRO's base, while the Tsviet Shelke has been betrayed द्वारा her comrades as she already completed her mission of finding Vincent's protomateria. Shelke reveals she has been connected with Lucrecia's memory allowing the WRO to complete Lucrecia's research of Omega. Based on Lucrecia's research, the group determines what Deepground has planned. Omega is a weapon, which activates when the planet senses that it is in mortal danger; the weapon causes the planet to gather the Lifestream and हटाइए to another planet, leaving the planet and everyone on it to die. Deepground plans to slaughter a large number of people at once to trick the planet into activating Omega early.
Vincent and the WRO launch a full-scale assault on Deepground's headquarters located in Midgar's remains with the assistance of various of their old comrades as well as Shelke. While Reeve's team battle the Deepground soldiers and destroying the reactors which serve as a mean to revive Omega, Vincent goes to Deepground's headquarters. During the assault, Vincent goes to the headquarters' bottom and finds the leader Weiss slumped in his throne, lifeless. As Omega starts merging with Weiss, the latter revives and confronts Vincent. It is revealed that Weiss is possessed द्वारा Hojo; before Hojo was killed in the Mako Cannon, he uploaded his consciousness into the worldwide network, then took possession of Weiss' body while he was online. Hojo and Vincent battle to a standstill; shortly after, Nero emerges from the Lifestream and pulls Hojo into the Lifestream. Nero then merges with the weakened Weiss in order to help him fuse with Omega.

As Hojo's spirit disappears, Omega is activated. While the WRO continues to fight the remnants of Deepground, Vincent is possessed द्वारा Chaos who stands around Omega. Shelke dives inside Omega to find Lucrecia's Protomateria and then give it to Vincent alongside Lucrecia's will, in which she explains Vincent's survival made her happy. Vincent then takes control of Chaos and battles Omega. After a battle with Omega and Weiss, Omega sprouts wings and tries to escape. Vincent charges Omega, creating an explosion which destroys the latter while the former disappears. As the lifestream returns to the planet, Vincent is found at Lucrecia's crystalline coffin in the Crystal Cave, stating that both Chaos and Omega were destroyed and thanking her for being his reason he survived. In the secret ending of the game, "G", a legendary warrior related with Deepground and Shinra, awakes beneath the ruins of Midgar, finding Weiss and leaving the ruins with him.