Mercenary Cloud Strife and his allies have prevented an apocalyptic attack from the psychotic Sephiroth, but human civilization remains in tatters. Furthermore, each member of Avalanche, the victorious rebel group, struggles with a growing emptiness and a lack of purpose in their new reality.

Cloud's childhood friend, Tifa Lockhart, who feels responsible for the loss of innocent lives, desperately tries to sustain her relationship with him. Still, the burden of their dead companions leads to a growing rift between them. Meanwhile, Barret Wallace and Red XIII search for a new ambition now that the threat of Sephiroth has passed, and Yuffie Kisaragi returns to her home nation of Wutai to help its citizens combat a new disease known as Geostigma.

But somewhere in the lifestream—the collective spiritual energy of the world and all who have died on its surface—lurks the remnants of Sephiroth's vengeful spirit, left to stew in its hatred toward Cloud and the rest of the human race. And while the soul of someone dear to Cloud monitors Sephiroth's growing animosity, the villain's revenge plot continues to spiral closer to completion.