SOLDIERs Zack Fair and Angeal are dispatched to Wutai to support Shinra in their war. In the outcome, Angeal disappears, and Zack is appointed go to find the other missing SOLDIER, Genesis, in the town of Banora. Zack and Tseng find that Genesis and Angeal have betrayed Shinra, but are forced to retreat as the village is destroyed by Shinra. Upon Wutai's war ending, Shinra's armies, as well as Zack and Sephiroth are assigned to kill Genesis and Angeal. Genesis creates an army of copies of himself to attack Shinra headquarters with help from Dr. Hollander who has sworn revenge against Shinra. After the forces are defeated, Zack and Sephiroth track down Hollander's secret laboratory in a Midgar mako reactor, and learn that Hollander, had used both Genesis and Angeal as part of Project G, an early attempt to create soldiers infused with Jenova Cells. They are found by Genesis and Hollander, with the former facing Sephiroth and the latter escaping as Zack chases him. Zack is stopped by Angeal intent on keeping Hollander alive as he wants to find a way to return to be normal, and knocks him into the slums of Midgar.
Zack recovers to find Aerith tending over him. After both spend some time together, Zack returns to SOLDIER headquarters which is being attacked by Genesis. On his way, Zack allies with Angeal who has hesitations about his actions. As Angeal, Zack and Sephiroth protect the headquarters, Angeal confronts Genesis, but both go missing once again. Zack is then ordered to investigate Modeoheim where Genesis has been spotted; en route, Zack meets Shinra infantry soldier Cloud, quickly becomes friends with him. Near Modeoheim, Zack encounters and defeats Genesis who then appears to commit suicide by throwing himself into the depths of a facility. Zack travels to Modeoheim and finds both Angeal and Hollander. Angeal mutates when attacked by copies of himself, and Zack is forced to kill him. Before he dies, Angeal gives Zack his Buster Sword, telling him to protect his honor. Zack, distraught over the death of his mentor, goes back to the Sector 5 church, where he is comforted by Aerith.
Sometime later, Shinra continues chasing Hollander who is protected by new Genesis' copies as the original is still alive. Zack returns to Midgar to protect Aerith after learning that they also appeared there, and leaves her with an Angeal copy that seems to be protecting her. Zack travels with Sephiroth and Cloud to investigate a mako reactor near Nibelheim. While checking the reactor Sephiroth discovers from Genesis that he was an experiment, implanted with cells of the extraterrestrial Jenova, but Sephiroth refuses. Genesis explains his body degrading and needs Sephiroth's cells which avoid his body to degrade, but he refuses. A week later, Sephiroth sets Nibelheim's town ablaze and goes to the Mako reactor to take Jenova's body. While Zack fails to stop Sephiroth, Cloud throws Sephiroth into Mako, causing his body to disappear. Zack awakes to find that he and Cloud have become part of Dr. Hojo's experiments on Jenova cells and Mako exposure; while Zack is unaffected by the Jenova cells, Cloud is unable to move on his own. Zack helps Cloud to escape and they quickly become high priority targets for the Shinra forces. While fleeing, Zack learns that Genesis and Hollander, the latter has become a Genesis copy, are still trying to stabilize his mutation. As Cloud is the only one carrying Sephiroth's pure cells due to the experiments, they plan to use him.
Hollander tries to reach Cloud, but is killed by Zack. Zack then finds Director Lazard who, now inflicted as an Angeal clone, tried to ally with Hollander to exact his revenge on Shinra. Lazard directs Zack to the remains of Banora to find Genesis, while Zack leaves Cloud with him. Zack enters into a cavern exposed to the Lifestream where he encounters Genesis who heals his body absorbing it and tries to kill Zack. Zack manages to defeat Genesis and returns to the surface with him. There, Zack finds that Shinra attacked Lazard and Cloud but the former was able to hold them back at the cost of his life. The Angeal copy that guarded Aerith had come to fight for Zack and was killed. Zack discovers a note he had carried from Aerith, and learns that he had been used as an experiment for more than four years. Zack takes Cloud to Midgar before Genesis is collected by two soldiers.
Shinra discovers Zack and Cloud on the barren terrain outside Midgar. Leaving Cloud hidden away, Zack goes off against an enormous number of Shinra troops, and is ultimately fatally wounded. Cloud manages to crawl to Zack's body after Shinra has left, and Zack, in his dying breath, bequeaths the Buster Sword to Cloud as Angeal had done to him. Cloud begins to walk back to Midgar, while Zack's body is taken to the Lifestream by Angeal. The epilogue recreates the opening scenes of Final Fantasy VII.
