- Cloud joins a group called AVALANCHE and they raid Mako reactors around the city of Midgar
- AVALANCHE is trapped during a raid at a reactor, which explodes and launches Cloud down below, falls, and meets Aeris
- When President Shinra's Turks operatives arrive, looking for Aeris to capture her, Cloud agrees to work for Aeris as her bodyguard
- Cloud and Aeris meet Tifa Lockhart and infiltrate crime boss Don Corneo's mansion
- He tells them that Shinra discovered the location of AVALANCHE's hideout and plans to collapse Sector 7
- Shinra successfully destroys Sector 7
- Turks capture Aeris, the last living member of the Cetra, which was previously thought to be extinct
- Shinra believes Aeris can lead him to the "Promised Land"
- The remaining members of AVALANCHE – Cloud, Tifa, and Barret – infiltrate Shinra's headquarters to rescue Aeris
- They free her and Red XIII, who joins them, and escape
- Most of the personnel in the building are killed, and Cloud suspects Sephiroth has returned
- These suspicions are confirmed by an executive who was spared and claims that Sephiroth said he would never allow Shinra claim the Promised Land
- During the massacre, the headless body of a creature named Jenova disappeared from the building
- AVALANCHE pursues Sephiroth for fear that his intentions for the Promised Land may be more destructive than Shinra's
- During this pursuit, Yuffie, Cait Sith, Vincent, and Cid join the party
- Sephiroth's plan is eventually revealed: Lifestream will gather together wherever the planet is significantly damaged to heal the wound, and he plans to create a fissure in the planet, enter it, and merge with the planet's energy to grant him god-like power over it
- Aeris sets off to stop Sephiroth from casting Meteor. AVALANCHE follows her, and witnesses Sephiroth kill Aeris. The remaining members of AVALANCHE vow to defeat Sephiroth to avenge her.
- The player soon learns that Jenova was an interstellar creature who traveled on a meteor and crashlanded on the planet 2,000 years ago, forming an impact crater. Jetra emerged from the crater and intededed to infect all living organisms with a virus. However, a small group of Cetras managed to defeat Jenova and confined it within the fissure created by its landing. Eventually, Jenova's remains are unearthed by Professor Gast, a research for the Shinra Company, who mistakes it for a Cetra and artifically produces a Cetra by combining cells from Jenova with the fetus of an unborn child.
- Five years ago from the present-day events, Sephiroth learned that he was the product of this experiment
- Sephiroth once again encounters Cloud. Suddently, an earthquake occurs and Cloud 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, who have begun to perceive everything as a threat to the planet. The members of AVALANCHE are interrogated, and eventually nearly executed. They escape from Junon and obtain Cid's airship, Highwind. They then search for Cloud. They discover Shinra's plan to take Huge Materia from the major spots of the world. Barret Wallace saves his hometown from Shinra's escort, thus redeeming himself for building the Mako reactor there in the first place. They eventually find Cloud, locating him on a tropical resort island called Mideel where he washed up following the casting of Meteor; he is in a catatonia|catatonic state. Unable to see Cloud like this, Tifa resolves that she will not leave Mideel until Cloud has fully recovered. The WEAPONs' destructive activity quickly causes the island to split open, depositing Cloud and Tifa into the Lifestream below. There, she reconstructs Cloud's memories and learns the truth about his past. Although the player learns he is a real human being and had actually been in Nibelheim during Sephiroth's attack, he never actually succeeded in joining SOLDIER and only managed to attain the rank of Private (rank)|private in Shinra's military. The player learns that the dark-haired SOLDIER is named "Zack Fair|Zack" and was Aeris' first boyfriend. During Sephiroth's destruction of Nibelheim, Zack, Tifa and Cloud fought Sephiroth in Nibelheim's Mako reactor. Although Tifa and Zack were defeated, Cloud and Sephiroth severely wounded one another. After decapitating the body of Jenova, which had been stored in the Mako reactor, Sephiroth is thrown into the Lifestream by Cloud, taking the creature's head with him. Rather than dying, however, his body and consciousness were crystalized in Mako inside Jenova's crater.
While Tifa was taken to safety in Midgar, Cloud and Zack were among the wounded survivors who were apprehended by Shinra as part an elaborate cover-up of Sephiroth's massacre. Professor Hojo subjected these survivors to an experiment, in which he performed the same enhancements given to members of SOLDIER. However, because Hojo conducted the experiment without any concern for the subjects' mental capacities to handle the procedure, all but Zack entered a comatose state. Nearly five years later, Zack broke free from his confinement and took Cloud with him. The player learns that the procedure used to enhance members of SOLDIER involved both Mako showers and the injection of cells from Jenova. The alien cells inhabiting Cloud's body allowed his mind to construct a false persona, built around Zack's behavior, fighting style, and description of Sephiroth's destruction in Nibelheim, but they also allowed Sephiroth to modulate his behavior. The cells' inherent ability to duplicate information led Cloud to believe he had been the 1st Class SOLDIER in Nibelheim, as Zack was killed outside Midgar by Shinra soldiers after saving Cloud's life, shortly before the beginning of FF7. During Zack's final moments, he tells Cloud to live "both of their lives" before taking his final breath. Afterward, Tifa discovered Cloud, who was wearing a Shinra Soldier 1st Class uniform, which Zack gave him at the Shinra mansion when they escaped from Hojo's experiment, and offered him a job with AVALANCHE.
With the truth revealed, Cloud awakens and rejoins AVALANCHE. Before he awakes, the few members of AVALANCHE recovered powerful magic, known as Huge Materia, to counter Shinra's attempts to destroy the WEAPONs and Meteor. During the next few segments, many members achieve their lifelong dreams, or settle their past. Cid Highwind became the first man in outer space, Yuffie Kisaragi encourages her father to return her hometown Wutai to its former glory, and Vincent Valentine learns the truth about his past. The player also learns that, in her final moments, Aeris was casting a spell known as "Materia#Holy|Holy", the only means of opposing Meteor. Though she succeeds, Sephiroth's focused will prevents the spell from taking effect and has been restraining it since. Deciding that humanity must be protected from the WEAPONs before Sephiroth can be approached, Shinra and AVALANCHE destroy the WEAPONs, but nearly all of Shinra's executives are killed in the process, seemingly including Rufus. Among the few survivors are Characters of Final Fantasy VII#Reeve|Reeve Tuesti, revealed to be the repentant controller of Cait Sith, 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. When Hojo attempts to help Sephiroth gain mastery over the Lifestream afterward, AVALANCHE is given no choice but to fight and kill him. Cloud tells the remaining members of his team to go find what they are fighting for. Every member returns, including Cait Sith, who had been captured by Shinra Inc. for helping Cloud.
Red XIII's grandfather dies, and tells him to go with Cloud to the final battle. With each member of Cloud's group at peace with their past and all other opponents defeated, the group travels through the Mantle (geology)|mantle of the planet to its core, where they defeat Sephiroth and free Holy. However, due to Meteor's already close proximity to the planet's surface, Holy is unable to destroy it alone. Selected as Meteor's target, Midgar is almost completely destroyed by the storms that spawn from its presence. However, sent by Aeris' spirit, the Lifestream itself rises from the planet to aid Holy by pushing Meteor away, allowing Holy to destroy it. During the epilogue that follows, Red XIII sprints through a canyon with his two cubs at his side, he proceeds up the cliff-face, which reveals a lush land of greenery, where the desolate landscape of Shinra's destroyed Midgar had once been. The fate of the rest of the team isn't revealed to the player. It is left purposely ambiguous.