Deviations from the original story::::
In Final Fantasy VII, Tifa's father is found already dead inside the mako reactor. In Last Order, he is found dying outside the reactor.
In Final Fantasy VII, when Tifa is injured by Sephiroth, Zack passes her. In Last Order, they have a conversation before Zack enters the chamber.
In Last Order, Cloud and Sephiroth have additional dialogue during their confrontation not present in the game.
In Final Fantasy VII, when Cloud charges Sephiroth with Zack's Buster Sword, Sephiroth turns in time to be stabbed in his stomach. In Last Order, Sephiroth is unaware of Cloud's presence in Jenova's chamber until after he is stabbed through his lower back.
In Final Fantasy VII, Cloud is impaled upon Sephiroth's Masamune once. In Last Order, he is stabbed with the sword twice.
In the original story, when Sephiroth attempts to leave with Jenova's head, Cloud pursues him onto a catwalk that crosses over the heart of the Reactor, a wide shaft leading into the Lifestream below. In this depiction of events, Sephiroth quickly turns and runs his Masamune through Cloud. After being impaled by Sephiroth and held in the air above the Lifestream, Cloud pulls the blade out of his chest and uses it to fling Sephiroth into the Lifestream. In contrast, in the OVA, Cloud charges Sephiroth while he stands at the top of the stairs leading to Jenova's chamber, and is impaled a first time. Sephiroth then tosses him into Jenova's room and impales him upon his blade a second time, holding Cloud's severely wounded body above the shaft that leads to the Lifestream (retconned to be in Jenova's chamber instead of another room). In this retelling of events, Cloud grasps the blade of Sephiroth's sword and throws him into a wall (which crumples from the force of Sephiroth's impact) instead, and Sephiroth then decides to jump into the Lifestream of his own free will. It should be noted that in the game, when Cloud reflects on the last time he saw Sephiroth, he states that "Sephiroth went off searching for the Promised Land, so he could become the ruler of the planet... That was 5 years ago... He told me he wants to go to the Promised Land with his mother, Jenova." These changes are also present in Before Crisis:Final Fantasy VII.
In the OVA, Cloud is shown with a strange glow in the eyes. This shows that in order to test a person's suitability to become a SOLDIER, they need to be infused with mako before they can be injected with Jenova cells. Obviously, Cloud's body had rejected mako infusion and thus he failed in becoming a SOLDIER, becoming only a grunt in the Shin-Ra army. But, in the OVA, it is shown that Cloud has a strong determination to fight with Sephiroth, so his body is able to react with mako (his eyes have a strange glow) that had been previously infused to him during the SOLDIER recruitment procedure. However, he was forcely infused with high levels of mako while he was inprisoned in the Shinra´s Mansion basement with Zack by Hojo and is also infused with Jenova cells later. Due to Cloud's body's rejection and not posessing the mental strength to handle the mako infusion process, he suffers mako poisoning and remains unconscious, as seen in the OVA.
In Final Fantasy VII, when Zack rushes Sephiroth, he is apparently defeated in one blow, or at the least, a very short period of time. In Last Order, he manages to trade several blows with Sephiroth over the course of 48 seconds before being bested. He is still ejected from Jenova's room and into a mako pod outside by Sephiroth's final blow, however.
In Last Order, after Cloud critically wounds Sephiroth and is moving Tifa to safety, she regains consciousness and speaks with him. In Final Fantasy VII, she does not. Instead, the dialogue seen in the OVA is spoken by Cloud and Tifa while they watch the flashback in the Lifestream. This is a plot hole, because in the game Tifa has no recollection of Cloud ever coming to Nibelheim 5 years ago, which is a key point to the story.
In Final Fantasy VII, Cloud is present during Sephiroth's attack on Nibelheim and is consequently knocked unconscious. He later recovers and rushes to the mako reactor after Zack has already gone in that direction. In Last Order, he discovers Nibelheim in flames along with Zack, and only goes to the reactor after scouring for injured civilians with Zangan. It is for this reason that he arrives at the reactor later than Zack in Last Order.
It had been previously speculated that the hidden scene on Disc 2 of Final Fantasy VII—accessible by visiting the Shinra Mansion's basement—happened only a few days before the opening events of the game's story. However, Before Crisis confirms that the two make their escape from Nibelheim a year before the opening events of Final Fantasy VII, and—as such—Turks recently added into continuity, yet not shown in the original Final Fantasy VII, are among Zack's pursuers.
In Last Order, Cloud and Zack are ambushed by Shin-Ra soldiers while hitchhiking to Midgar in a pickup truck. While the original game featurs the hitchhiking scenario, it does not feature the attack that Cloud and Zack suffer at that time. In the retelling of events, Zack is shot while taking a bullet meant for Cloud. This is speculated to have left him wounded and less able to defend himself when he and Cloud reach their fated destination: a bluff overlooking Midgar, where Zack is gunned down and killed.