The survivors of Midgar have begun to build a new city, Edge. A strange disease known as "Geostigma" has arisen. After Cloud's showdown with Sephiroth, he has been living with Tifa in Edge. Cloud is attacked by three men, Kadaj, Loz, and Yazoo, who believe that he has hidden their "mother". At the meeting place, Cloud discovers that Rufus Shinra is still alive. Kadaj arrives and demands that Rufus tell him where to find his "mother". It is revealed that his "mother" is Jenova's remains, and is somehow connected to the cause of the Geostigma.

The trio are planning a new "reunion" that will culminate in an assault on the Planet. Loz arrives at Aerith's church in Midgar in an attempt to find Jenova's remains. After battling Tifa, he receives instructions on his cell phone to capture Marlene. Kadaj and the gang begin collecting children infected with Geostigma, including Denzel and the uninfected Marlene, and take them to the Forgotten City. Cloud attempts to rescue them but fails, and is quickly defeated, and is then rescued by Vincent Valentine, who reveals to Cloud what the trio is seeking and that it could result in the return of Sephiroth. Cloud agrees to return to Edge and face Kadaj in battle. Cloud and his friends are able to dispatch the monsters and Bahamut SIN. Kadaj spots Cloud in pursuit of him, and is followed to the ruins of Midgar. They battle each other in Aerith's church. Kadaj destroys the flowerbed, which releases an outflow of Lifestream-infused water that cures Cloud's Geostigma. Kadaj absorbs Jenova's remains into his body, allowing Sephiroth to be reborn through the Remnant's body. Sephiroth reveals that once those who die from the Geostigma return to the Lifestream, he will be able to control it and use the Planet as a vessel to travel space in search of a new planet for him to rule. Cloud defeats Sephiroth who dissipates leaving a weakened Kadaj at Cloud's mercy. Aerith begins to pour healing rain across Edge, curing the people of their Geostigma. Cloud awakens in a pool of Lifestream-infused water in Aerith's church, surrounded by his friends, family and the citizens of Edge. After curing the Geostigma-infected Denzel, he turns and sees Aerith crouching by some children. As she stands and walks to the doorway, she turns back and says that everything's all right now, and steps into a white light with Zack. Cloud says that he now knows that he's not alone.

Opening line: To those who loved this world and knew friendly company therein. This reunion is for you.

Marlene Wallace: There was one SOLDIER named Sephiroth, who was better than the rest. But when he found out about the terrible experiments that made him, he began to hate Shinra. And then, over time, he began to hate everything. Shinra, and the people against them. Sephiroth, who hated the planet so much that he wanted to make it go away. And the people who tried to stop him. There were a lot of battles. For every battle, there was more sadness. Someone I loved went back to the lifestream too. And then it came; the chosen day. In the end, the planet itself had to make the battle stop for good. The planet used the lifestream as a weapon and when it burst out of the earth, all the fighting, all the greed and sadness, everything was washed away. Sadness was the price to see it end.

Kadaj: Brother! I'm with her at last.
Cloud: So what's gonna happen now?
Kadaj: Mother's going to tell me.
Cloud: I guess a remnant wouldn't really know.
Kadaj: So what if I'm a puppet? Once upon a time.

Aerith Gainsborough: You came. Even though you're about to break. That's a good sign.

Yazoo: Hey Kadaj, is that where big brother lives?
Kadaj: Yeah.
Yazoo: Do you think he will be glad to see us?
Kadaj: Not a chance.
Loz: Don't cry, Yazoo.

Marlene Wallace: Does Cloud live here?
Tifa Lockhart: I guess he does.

Cloud: I was right. I'm no good to anyone. Vincent. What do you know about this?
Vincent Valentine: I come here often.

Vincent Valentine: The stigma... it's a symptom of alien matter infesting the body. When it tries to eliminate it, it overcompensates. Inside our bodies there's a current, like the Lifestream. That current is what fights off any malevolent intruders.

Aeris Gainsborough: Why can't you forgive yourself?

Cloud: Tifa, I'm not fit to help anyone. Not my family, not my friends, nobody.
Tifa Lockhart: Dilly-dally, shilly-shally!
Reno: I think she wants you to move on, man.

Tifa Lockhart: Two years ago, think of the strength we all had when we fought that last battle. It's only been a couple of years, but already that feeling is gone. But Cloud, I think he's found it again.

Yuffie Kisaragi: What? I don't get it! Why can't we help out?
Cid Highwind: This is Man Talk.
Yuffie Kisaragi: Sexist!

Cloud: Stay where you belong; in my memories!
Sephiroth: I will... never be a memory!

Rude: Shinra technology at its finest.
Reno: Oh, so you made it?
Rude: If nothing else, it's flashy.

Cloud: I only came for the kids.
Kadaj: See this man? He's our big brother. But alaso, in our happy flock, he's what you'd call a "Black Sheep."

Rufus Shinra: The Lifestream courses through our Planet back and forth across the borders of life and death. If that cycle is the very truth of life then history, too, will inevitably repeat itself. So go on - bring your Jenovas and your Sephiroths.
Kadaj: Please, sir, is that your excuse for going after Mother yourself? You don't seem all that sorry.
Rufus Shinra: Sorry? Why, I've never had this much fun.