The game begins with a flashback to the ending of Final Fantasy VII. As Meteor looms overhead, Yuffie and Vincent are in Midgar helping with the evacuation. Vincent tells Yuffie to check the Mako Cannon. She does so, and the device she is using finds a single person still alive there. Despite Yuffie's protests, Vincent ascends the Cannon to the firing controls to find the slumped body of Hojo. Vincent trains his triple-barreled handgun, Cerberus, on him but, just as he is about to fire, an explosion blows Hojo's body away and causes the tower to start crumbling. Vincent is narrowly rescued by Yuffie on a hovercraft, after which they rendez-vous with Cloud and the others.
Three years later, in the Waterfall Cavern, Vincent sits with his lost love Lucrecia Crescent, her body encased in Mako Crystal. She speaks to him telepathically, apologizing, though Vincent doesn't know why, claiming he is the one who should apologize. This exchange is revealed to be a brief flashback, and Vincent is actually sitting alone in a hotel room in Kalm, where a celebration is taking place to commemorate the three-year anniversary of Meteorfall. A nearby television shows a news report about a recently uncovered entrance to an unknown part of the Shinra complex deep underground, where it is rumored a force of soldiers more powerful than SOLDIER were created.