Three years after the destruction of Midgar, a mysterious organization has emerged from the wreckage of the Meteor disaster. The survivors are the savage Deepground soldiers, and they bring with them an end to the short-lived peace the world had enjoyed. When Vincent Valentine finds himself hunted by an elite group of the soldiers, he once again becomes embroiled in a battle for the planet... but this time, the secrets to his past may be awaiting discovery...

The story of Last Order: Final Fantasy VII alternates between two different time periods.

The first tells of Zack and Cloud's escape from ShinRa capture approximately a year before the events of Final Fantasy VII. Through a series of loosely connected scenes, Zack aids a nearly comatose cloud in a year-long quest to reach relative safety in Midgar. In the end, he is fatally wounded protecting Cloud, shortly before Final Fantasy VII's beginning.

The second scenario provides an expanded look at the Nibelheim incident, in which Sephiroth razes the town and seeks out JENOVA in the Mako Reactor. Tifa Lockheart is seriously injured attempting to attack Sephiroth with his own sword. Attempting to come to her rescue, SOLDIER 1st Class Zack Flair is beaten in battle by Sephiroth. But then, lowly soldier Cloud Strife stabs Sephiroth with Zack's Buster sword. Even such a mortal injury isn't enough to finish Sephiroth off, and Cloud soon finds himself impaled on the end of Sephiroth's sword, dangling above the pit leading down to the lifestream. Despite the injury, Cloud pulls himself along the edge of the blade and uses it to hurl Sephiroth against a wall. Sephiroth then jumps into the Lifestream with JENOVA's head to seek out the Promised Land.

The two stories are connected by the reflections of Turk leader Tseng, who was at the Mako reactor when Zack and Cloud, both seriously wounded, were taken away for testing and captivity under the care of Professor Hojo. He is in charge of dealing with the two when they make their escape four years later, and though he orders the Turks to capture the two alive if at all possible, rogue ShinRa soldiers fire the mortal shots that lead to Zack's demise.