Two years have passed since Cloud Strife defeated Sephiroth, who attempted to damage the planet by summoning a meteor. Cloud has been living withTifa Lockhart in a city called Edge, and both have been taking care of Marlene, their friend Barret Wallace's daughter, and the orphan Denzel. Cloud and many other citizens are infected by a strange new disease known as "Geostigma". Cloud is on his way to meet the Turks, a group that performs operations with the megacorporation Shinra. He is attacked by three men—Kadaj, Loz, and Yazoo—who believe that he has hidden their "mother". Kadaj ends the battle when he discovers that Cloud does not have her. When he arrives at the meeting place, Cloud discovers that Shinra's president, Rufus Shinra, survived the events of the original title. Rufus attempts to enlist Cloud's help to stop the trio, but Cloud refuses. Kadaj arrives and demands that Rufus tell him where to find his mother. It is revealed that his mother is the remains of Jenova, an extraterrestrial lifeform whose cells were injected in Sephiroth's body and helped him in Final Fantasy VII, and is connected to the cause of the Geostigma. The trio are planning a reunion with Sephiroth that will culminate in an assault on the Planet.
Loz arrives at the church of the late Aerith Gainsborough in Midgar to look for Jenova's remains, where he is confronted by Tifa. After defeating Tifa, he captures Marlene under Kadaj's orders. Yazoo begins collecting children infected with Geostigma, including Denzel, telling them they will be healed; he takes them to the Forgotten City. Cloud goes there to rescue them after getting the information from the Turks. In the Forgotten City, Cloud battles the gang but is overpowered; he is rescued by his former comrade Vincent Valentine. Vincent tells Cloud what the trio is seeking and that it could result in the return of Sephiroth. Cloud finds Marlene and returns to Edge to face Kadaj's gang. The trio call forth several monsters, including the enormous creature Bahamut SIN,[1] to attack the populace who are trying to rescue the kidnapped children. Turks Reno and Rude try to deal with Yazoo and Loz who are searching for Jenova's remains in the city's monument as informed by Rufus. After rescuing Denzel, Cloud, Tifa and their old companions dispatch the monsters and Bahamut SIN.
In a nearby building, Rufus tells Kadaj that he has been in possession of Jenova's remains all along. He throws the box containing the remains from the edge of the building. Kadaj recovers the remains shortly after Rufus shoots and damages them. Cloud pursues the trio to the ruins of the city of Midgar. Yazoo and Loz are caught in an explosion, and Cloud catches Kadaj. In Aerith's church, an outflow of water infused with Lifestream, the planet's life force, cures Cloud's Geostigma. Vincent explains to the group that Kadaj's gang are remnants of Sephiroth, which makes them decide to leave them to Cloud due to his previous fights against Sephiroth. Outmatched by Cloud in battle, Kadaj absorbs Jenova's remains into his body, which allows Sephiroth to reappear. Sephiroth tells Cloud that once those who die from the Geostigma join the Lifestream, he will be able to control the planet and use it as a vessel to travel in search of a new planet to rule, in the same way Jenova did. Cloud defeats Sephiroth, who dissipates, leaving a weakened Kadaj at Cloud's mercy. After Kadaj's death, a healing rain starts falling across Edge, curing the people of their Geostigma. Cloud is confronted by Yazoo and Loz who are also succumbing to the healing rain. Both prepare one last attack at Cloud as he charges at them, resulting in a large explosion that engulfs all three.
Afterward, Cloud appears surrounded by a white light, and Aerith and his late friend Zack Fair are heard, telling Cloud that his place is not with them yet. Cloud awakens in a pool of Lifestream-infused water in Aerith's church, surrounded by his friends, and the citizens of Edge. After curing Denzel and the other infected children with the water, he turns and sees Aerith and Zack leaning against the doorway. As they step into white light, Aerith says "You see, everything's all right", and Cloud replies, "I know... I'm not alone... not anymore".
