Two years after Meteorfall, an event averted by the rebel group AVALANCHE, the world remains scarred, plagued by Geostigma, a mysterious disease with no known cure. Amidst this turmoil, Rufus Shinra, president of the fallen Shinra Electric Power Company, seeks answers. Suspecting a connection between Geostigma and the alien entity Jenova, Rufus orders his Turks to recover Jenova’s head from its last known location in the Northern Cave. Their mission goes awry when a hostile force abducts two of their members.
Meanwhile, Cloud Strife, a former AVALANCHE operative, lives in the newly constructed city of Edge with Tifa Lockhart and two children, Marlene Wallace and Denzel, the latter afflicted with Geostigma. Cloud, burdened by guilt over the deaths of Zack Fair and Aerith Gainsborough, has distanced himself, anticipating his own demise as the disease ravages his body. While on a delivery through the Midgar Wasteland, Cloud is ambushed by three enigmatic figures on motorcycles: Kadaj, Loz, and Yazoo—the Remnants of Sephiroth. They seek their “mother,” Jenova, to initiate the Reunion, a plan to resurrect Sephiroth.
Rufus contacts Cloud, requesting his aid in stopping the Remnants. Cloud, struggling with his own inner demons, refuses. Shortly after, Kadaj invades Rufus’s headquarters, abducting him and revealing plans to use Jenova’s remains to bring Sephiroth back. While Kadaj holds Rufus captive, his brothers Loz and Yazoo descend on Edge. Loz defeats Tifa and kidnaps Marlene, while Yazoo lures Geostigma-infected children, including Denzel, by promising a cure.
Cloud returns to the ruins of the Sector 5 slums church to find Tifa unconscious and Marlene missing. Succumbing to his illness, Cloud collapses but is rescued by Reno and Rude of the Turks. Back at the 7th Heaven Bar, Tifa confronts Cloud about his self-destructive behavior, urging him to face his guilt. Despite this, Cloud remains paralyzed by doubt. Meanwhile, the Remnants corrupt the waters of the City of the Ancients, forcing the abducted children to drink and fall under their influence.
On his way to rescue the children, Cloud is visited by Aerith’s spirit, who questions his refusal to move on from her death. Encouraged by her words, Cloud presses forward but fails in his attempt to save the children. He is rescued by Vincent Valentine, who reveals the Remnants’ true intentions and confirms the survival of Tseng and Elena, Turks who were tortured during their mission in the Northern Cave. Vincent’s confession about his own inability to move on from his past inspires Cloud to confront his fears.
As the Remnants rally the children to dig beneath the Meteorfall Monument in Edge, hoping to uncover Jenova’s head, Reno and Rude intervene, engaging Loz and Yazoo in battle. Kadaj summons Bahamut SIN, a monstrous summon, to destroy the monument. The summon rampages through Edge, but Cloud, joined by his former AVALANCHE comrades, defeats the creature. Rufus then reveals he has been hiding Jenova’s head all along. In a dramatic confrontation, Rufus tosses the box containing Jenova’s remains off the edge of a building. Kadaj retrieves it, sparking a high-speed chase through Edge and onto the Midgar Expressway. With Reno and Rude’s help, Cloud dispatches Loz and Yazoo, leaving only Kadaj.
Kadaj flees to the Sector 5 church, where Cloud confronts him. As Lifestream-infused water erupts from the flowerbed, Aerith’s presence cleanses Cloud of his Geostigma. Renewed and determined, Cloud pursues Kadaj to the ruins of the Shinra Building in Midgar. There, with the support of his AVALANCHE allies, Cloud battles Kadaj, who uses Jenova’s remains to complete the Reunion, transforming himself into Sephiroth.
Sephiroth declares his plan to use the corrupted Lifestream, filled with the souls of Geostigma’s victims, to dominate the planet and journey to a new world. In a fierce battle above the ruins of Midgar, Sephiroth overpowers Cloud, leaving him gravely injured. As Sephiroth moves to deliver the final blow, Cloud has a vision of Zack’s spirit. Zack reminds Cloud of his strength, calling him his living legacy and encouraging him to fight. Bolstered by Zack’s words, Cloud unleashes Omnislash Version 5, defeating Sephiroth, who fades away with a cryptic promise: “I will never be a memory.”
With Sephiroth’s will dissipated, Aerith’s rain cleanses the planet of Geostigma. As Kadaj dissolves into the Lifestream, Yazoo and Loz ambush Cloud, fatally wounding him before triggering a massive explosion. Cloud awakens in a vision of the Lifestream, greeted by Aerith and Zack. They assure him his time has not yet come, urging him to return to the living.
Cloud regains consciousness in the Sector 5 church, surrounded by his friends and the children he saved. Reunited with his community, Cloud finally embraces the present, letting go of his guilt and grief. As Aerith and Zack’s spirits bid him farewell, Cloud looks ahead with renewed hope, ready to live his life free from the shadows of the past.
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