In the epilogue, Shelke, sitting inside Seventh Heaven, narrates that life has begun to return to normal, and that she seems to be beginning to age again. Yuffie bursts in, asking Tifa if she's heard from Cloud regarding "him"; Tifa replies that she hasn't. Shelke is seen to be speaking into a cassette recorder. Meanwhile, Vincent is inside the Waterfall Cavern speaking to Lucrecia. He tells her that both Omega and Chaos have returned to the Lifestream until they are actually needed. Before leaving, he thanks her, saying that "[she was] the reason [he] survived". Unseen by Vincent, a tear rolls down Lucrecia's cheek. Exiting the cavern, Vincent is surprised to find Shelke looking in the distance. Without looking round, she tells him that everyone is waiting for him, and that they made her come and get him, "not that [she minds], though". They look to the sky together, where fragments of Omega remain, floating in space.

If the player collected all three G Reports, a secret ending sequence shows the emergence of Genesis Rhapsodos in a cave where he finds the body of Weiss, carries it into his arms and, saying that "it is not yet time for slumber" and that "[they] still have much work to do", as well as calling Weiss "[his] brother", unfurls his lone black wing and flies away.