A veteran samurai, who has fallen on hard times, answers a village's request for protection from bandits. He gathers 6 other samurai to help him, and they teach the townspeople how to defend themselves, and they supply the samurai with three small meals a day. The film culminates in a giant battle when 40 bandits attack the village.

Two years after the events in "Final Fantasy VII", a disease called 'Seikon-Shoukougun', or 'Geostigma', is spreading through the planet. This disease is believed to have been caused by the body fighting off foreign material that invaded the body two years earlier, at the end of "Final Fantasy VII". Guilt-ridden and haunted by his past, ex-SOLDIER Cloud Strife has decided to live a secluded, solitary life away from his friends while maintaining "Strife's Delivery Service", whose headquarters is located in Tifa Lockheart's bar, the Seventh Heaven. Tifa's bar serves as an orphanage for children stricken with Geostigma. Here, Tifa keeps an eye on Barret's six-year-old daughter, Marlene, while Barret searches the planet for an alternative energy source to the Planet's energy, Mako. One day, Cloud receives a phone call from the former Shinra, Inc. president, Rufus, asking him for protection from a mysterious man named Kadaj. Kadaj, in the meantime, along with his brothers Loz and Yazoo, are searching for their "mother", and seem to believe that Cloud knows where to find her. Meanwhile, Vincent Valentine has been wandering the planet gathering information on Kadaj's scheme, and Cloud and his friends must come together again to fight these new enemies.

High school student Ling Xiaoyu is recruited by Anna Williams of G Corporation to transfer to Kyoto University and gather information on a student named Shin Kamiya. Meanwhile, Jin Kazama, the current head of the Mishima Zaibatsu, sends Alisa Bosconovitch to the university for the same mission. Though they do not know each other's true motives, Xiaoyu and Alisa become close friends. However, their friendship is put to the test when Shin is captured by an unknown assailant.