Final Fantasy XIV begins with Cloud joining AVALANCHE in a series of raids against the Mako reactors surrounding the city of Midgar. Although the first mission is successful, AVALANCHE is trapped at another reactor during a subsequent raid. The reactor explodes, launching Cloud from the upper levels of Midgar into the slums below. He lands on a flower bed, where he is formally introduced to Aeris.[22] Prompted by the arrival of Shinra's Turks operatives sent to capture Aeris, Cloud agrees to be Aeris' bodyguard and defends her from the Turks.[23] After the Shinra discover the location of AVALANCHE's hideout,[24] they destroy it by demolishing the entirety of Sector 7, killing its population and three members of AVALANCHE. The Turks also capture Aeris, who is revealed to be the last surviving "Cetra",[25] a race closely attuned with the planet and previously thought extinct. President Shinra believes Aeris can lead him to the "Promised Land", a mythical land of fertility, where he expects to find Mako energy.[26]

The remaining members of AVALANCHE infiltrate Shinra corporate headquarters to rescue Aeris. After freeing her and Red XIII, they escape because most of the personnel in the building, including the president, are killed by Sephiroth, a man presumed to be dead, who stated that he would never allow Shinra to claim the Promised Land.[27] The party also learns that during Sephiroth's attack on Shinra, the headless body of a creature named "Jenova" disappeared from the building's research facility.[28] While the president's son, Rufus Shinra, assumes control of the company, AVALANCHE pursues Sephiroth across the planet, fearing his intentions for the Promised Land may be more destructive than Shinra's. The party is joined by Cait Sith and Cid Highwind, and optionally by Vincent and Yuffie. The full scope of Sephiroth's plan is eventually revealed: if the world is significantly damaged, the Lifestream will gather in an attempt to heal the wound. Sephiroth intends to use a powerful spell called "Meteor" to cause this injury, and then merge with the planet's energy, allowing him to be reborn as a god and rule over the planet.[29] Aeris sets off to stop Sephiroth on her own. AVALANCHE follow her to the northern continent, where they enter an ancient Cetra city. After finding Aeris praying to the planet for aid, Sephiroth impales Aeris with his sword himself.[30]
Sephiroth kills Aeris in a scene which has been referred to by some as "the most shocking moment in video games".[18]

Influenced by Sephiroth, Cloud becomes suspicious of his memories and insists he is not a real human, but instead a specimen created from Jenova's genetic material by Professor Hojo. Jenova was an interstellar creature who crash landed on the planet roughly 2,000 years prior to the game's events. Jenova had intended to infect all living organisms on the planet with a virus inducing insanity and monstrous transformations;[31] among its victims were most of the Cetra. Attempting to defend itself, the planet created giant monsters called "WEAPONs". The majority of humans fled rather than fight Jenova; however, a small group of Cetra survivors managed to defeat and confine Jenova.[32] Eventually, the remains of Jenova were unearthed by Professor Gast, a researcher for the Shinra Company. Mistaking the creature for a Cetra, Gast was given authorization to conduct an experiment to artificially produce a Cetra by combining cells from Jenova with the fetus of an unborn child.[31] Sephiroth learned that he was the product of this experiment while on a Shinra mission in Cloud and Tifa's hometown, Nibelheim. He concluded that he was a Cetra who had been produced solely from Jenova's genetic material. He burned down Nibelheim, intending to kill all descendants of those he believed had abandoned his ancestors in the defense of the planet. Cloud confronted Sephiroth during this massacre, after which Sephiroth vanished under unknown circumstances and was presumed dead until his reappearance in the Shinra building. When AVALANCHE travels to the Northern Crater to confront Sephiroth, he tells Cloud that he was not in Nibelheim, showing him images of a SOLDIER with dark hair who occupies Cloud's place in his memories.[33] Tifa is unable to refute Sephiroth's claims, and Sephiroth casts the Meteor spell, causing the planet to awaken the WEAPONs in response. During the earthquake that follows, Cloud is separated from his companions and falls into the Lifestream.

As the meteor summoned by Sephiroth slowly approaches the planet, the Shinra Company focuses its efforts on protecting humanity from the WEAPONs, as well as defeating Sephiroth, in the hopes that this will dismiss Meteor itself.[34] Meanwhile, the members of AVALANCHE find Cloud in a catatonic state on a tropical resort where he washed up following the casting of Meteor. The WEAPONs' destructive activity causes the island to split open, and Cloud and Tifa fall into the Lifestream, where she reconstructs Cloud's memories and learns the truth about his past. It is revealed that Cloud never succeeded in joining SOLDIER, and that the dark-haired SOLDIER from his memories was actually Aeris's first love and Cloud's best friend, Zack Fair. Zack, Tifa, and Cloud had fought Sepiroth during the burning of Nibelheim. Although Tifa and Zack were defeated, Cloud and Sephiroth severely wounded one another. After decapitating Jenova, Sephiroth was thrown into the Lifestream by Cloud, taking the creature's head with him. Rather than dying, his body and consciousness were crystallized in Mako inside Jenova's crater.

Cloud and Zack were among the wounded survivors who were apprehended by Shinra as part of a cover-up of Sephiroth's massacre. Professor Hojo subjected these survivors to an experiment, performing the same enhancements given to SOLDIER members—a procedure which included Mako showers and the injection of Jenova cells. All but Zack entered a comatose state, and nearly five years later, Zack broke free from his confinement and took Cloud with him. However, the alien Jenova cells in Cloud's body still allowed Sephiroth to modulate his behavior. Moreover, the cells' ability to duplicate information allowed Cloud's mind to construct a false persona built around Zack's behavior. This was prompted by Zack himself, who was killed outside Midgar by Shinra soldiers during the escape; he urged Cloud to live both their lives before passing on. Afterward, Tifa discovered Cloud, who was wearing a SOLDIER 1st Class uniform, and offered him a job with AVALANCHE.[31]

After Cloud awakens, it is revealed that Aeris, in her final moments, was casting the spell "Holy" with the White Materia, the only means of opposing Meteor. Although she succeeded, Sephiroth had since prevented the spell from taking effect. Deciding to protect humanity from the WEAPONs before approaching Sephiroth, Shinra and AVALANCHE destroy the WEAPONs, although nearly all of Shinra's executives are killed in the process. Among the few survivors are Reeve Tuesti, who is revealed to be the repentant controller of Cait Sith,[35] and Professor Hojo, who is revealed to be Sephiroth's biological father. He explains that he and his wife were assistants to Professor Gast, and offered up their unborn child as a test subject to research involving Jenova.[36] After finding out that Hojo is trying to help Sephiroth gain mastery over the Lifestream, AVALANCHE kills him. In their final assault against Sephiroth, the group travels through the Northern Crater to the planet's core. They defeat Sephiroth and free Holy, but the spell is unable to destroy Meteor alone. Selected as Meteor's target, Midgar is almost completely destroyed. However, the Lifestream rises from the planet to aid Holy in destroying the Meteor.[37] During the epilogue, taking place 500 years after the game's events, Red XIII runs through a canyon with two cubs at his side. He proceeds up a cliff-face, which reveals a lush land of greenery where Midgar had once been.

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