Final Fantasy: Dirge of Cerberus (Nintendo Cinematic Universe)

Final Fantasy: Dirge of Cerberus is a Japanese anime film.

Summary
Vincent is targeted by Deepground, a mysterious organization that plans to awaken a creature known as Omega, with the ability to destroy the Planet.

Plot Elements

 * As Vincent and Yuffie Kisaragi help to evacuate Midgar, which is about to be destroyed by Sephiroth's Meteor spell, Vincent finds the body of Professor Hojo slumped at the controls of the Sister Ray cannon.
 * After a flash of lightning, Hojo's body seems to disappear, and before Vincent can investigate, the cannon explodes, forcing Vincent to escape with Yuffie.
 * Three years later, Vincent is in the town of Kalm when it is attacked by a group of mysterious soldiers.
 * Vincent, with the help of his former comrade, Reeve Tuesti of the World Regenesis Organization (WRO), an organization dedicated to helping the planet recover, fights the soldiers and forces them to retreat, but not before many of the citizens of the town have been captured, and many more killed.
 * Reeve explains to Vincent that the soldiers were members of Deepground, a military organization created as part of a covert Shinra operation to create genetically enhanced super soldiers.
 * Vincent soon learns that he is one of Deepground's primary targets, as he is unknowingly in possession of "Protomateria", a substance which he uses to control the "Chaos" gene hidden inside him.
 * Deepground claims they need the Protomateria to control "Omega".
 * According to ancient tablets discovered some years previously, Chaos and Omega have an unknown but important relationship, with Chaos described as "Omega's squire to the lofty heavens." The Chaos gene was injected into Vincent over thirty years previously by the scientist Lucrecia Crescent, Hojo's research assistant, with whom Vincent was in love.
 * In an effort to find answers, Vincent goes to the town of Nibelheim where Lucrecia studied Omega and Chaos.
 * Whilst at Lucrecia's research lab, Vincent is ambushed by Rosso the Crimson, who steals the Protomateria but is prevented from killing Vincent by the arrival of Yuffie. As they return to the WRO headquarters, they find that Deepground has launched an assault on the base. However, Deepground member Shelke the Transparent has been captured by the WRO, and reveals that she is synaptically interconnected to Lucrecia's memories, thus allowing the WRO to complete Lucrecia's research on Omega.
 * Shelke's sister, Shalua Rui, a high-ranking scientist in the WRO, soon discovers that Omega is a WEAPON, which activates when the Planet senses that it is in mortal danger.
 * Omega's function is to absorb the Lifestream from the Planet and then move to another planet, leaving the inhabitants behind to die. Deepground plans to slaughter a huge number of people at once so as to 'trick' the planet into activating Omega prematurely.
 * Vincent and the WRO launch a full-scale assault on Deepground's headquarters in Midgar.
 * While Reeve's team battles the Deepground soldiers and attempt to destroy the Mako reactors which serve as a means to revive Omega, Vincent heads to Deepground's centre of operations to confront Weiss. He is surprised to find Weiss slumped in his chair, dead. However, as Omega begins to manifest itself, Weiss seems to revive, and confronts Vincent.
 * It is revealed that Weiss is possessed by Hojo; before Hojo was killed in the Mako Cannon three years earlier, he uploaded his consciousness into the Worldwide Network, then took possession of Weiss's body while he was online attempting to find a cure for the virus with which the Restrictors had infected him.
 * Hojo/Weiss and Vincent battle to a standstill. However Nero, who had been defeated earlier by Vincent, emerges from the Lifestream and destroys Hojo.
 * Nero then merges with Weiss in order to help him fuse with Omega, just as Vincent is fused with Chaos.
 * While the WRO continues to fight the remnants of Deepground, Vincent transforms into Chaos in a desperate attempt to defeat Omega Weiss.
 * Shelke dives inside Omega to find Lucrecia's Protomateria, and upon finding it, she gives it to Vincent, also telling him that his survival made Lucrecia happy. Vincent then takes control of Chaos and battles Omega.
 * Omega sprouts wings and tries to ascend from the planet, but Vincent manages to destroy it, disappearing in the process.
 * A week later, he is seen visiting Lucrecia's crystalline tomb in the Crystal Cave. He states that both Chaos and Omega have returned to the Planet, and he thanks Lucrecia for being the reason he survived. He is then found by Shelke outside the cave, and she tells him that everyone else is waiting for him.
 * Post-Credits Scene: "G", a legendary warrior with unexplained connections to Deepground, awakes beneath the ruins of Midgar. He finds Weiss's body and picks it up. He tells the dead Weiss, "It is not yet time for slumber. We still have much work to do... My brother." He then sprouts a large black wing and flies into the night carrying Weiss with him. The Crisis Core Ultimania, however, explains that "G" (Genesis) has returned from his three-year slumber to protect the Planet.