Advent Children opens with a faithful remake of the "500 Years Later" FMV from the very end of Final Fantasy VII. From there, it goes back 498 years (or two years after Meteor) to the film's main setting. A Shinra helicopter hovers above the Northern Crater, where Tseng and Elena are looking for something. After finding what they're after, they are attacked, and the helicopter, piloted by Reno, manages to get away.
The next sequence is a recap of the main events of Final Fantasy VII, as narrated by Marlene: the Shinra's use of energy from the Lifestream, Sephiroth's hatred, and the battle to save the Planet. We then cut to the present day city of Edge, which has been built adjacent to Midgar. In the center of this city stands a Meteor memorial statue. A disease called "Star Scar Syndrome", or Geostigma, affects many of the residents, including orphaned children.
Inside the rebuilt Seventh Heaven, Marlene watches over a Geostigma-afflicted orphan named Denzel, while Tifa answers a ringing phone. Tifa then calls Cloud, who is out in the wastelands and is himself afflicted by Geostigma. The call Tifa got was from Reno at the Healin Lodge; it seems the Turks have a job for Cloud. As Cloud starts off for the Healin Lodge on his motorcycle Fenrir, three black-clad men with silver hair watch him leave from afar. They are Kadaj, Yazoo, and Loz, and they're on the hunt for their "Mother". Believing that "big brother" Cloud might have her, Yazoo and Loz rush down on their motorcycles to attack him, while Kadaj watches the proceedings and talks to someone on his cell phone. Cloud's attackers eventually retreat, and he continues to the Healin Lodge, voicemail messages from Barret and Tifa playing in the background.
At the Healin Lodge, after a brief confrontation against Reno and Rude, Cloud is surprised to find himself face to face with Rufus, who is now confined to a wheelchair and mostly concealed by white cloth. Rufus tells Cloud that he wishes to hire him and that he wants to make up for all of the misery that Shinra has caused the world. He also talks about the trip to the Northern Crater, saying that although the Turks found nothing, Kadaj and his buddies interfered with the mission. Cloud ends up rejecting Rufus' offer to become his bodyguard, and leaves.
Meanwhile, Tifa and Marlene are checking out the church in Midgar's Sector 5. They discover that Cloud has been living there, and also find a stained bandage among his belongings. Until then, neither of them knew Cloud was sick. They decide to stick around to wait for Cloud to return.
Back at the Healin Lodge, Kadaj has arrived and defeated Reno and Rude. Under this pressure from Kadaj, Rufus says he'll tell the truth this time—that "it" fell from the helicopter during their escape. Kadaj doesn't believe this, and tosses out Tseng and Elena's blood-spattered Shinra Company IDs. Kadaj then reveals his goal: he wants Mother's power for the Reunion and to get revenge on the Planet. Geostigma is tied into this Reunion, but it's not enough for Kadaj.
Cloud stands on Midgar's outskirts with an old, rusty Buster Sword. Memories of his friend Zack come to him, and his Geostigma flares up.
Back at the church, Loz arrives, asking about Mother. Tifa says there's no one here, and after Marlene runs off and hides, Tifa and Loz duke it out. After delivering a punishing blow to Loz, Marlene comes out of hiding. Then, a cell phone goes off. Loz gets up and answers it, saying that it's not here. Round Two of the battle starts, and Tifa is defeated. Loz is about to deliver the final blow when he's hit by a materia, thrown by Marlene, who is standing next to a metal chest full of the stuff.
In Edge, Denzel is sitting outside when a girl carrying a stuffed moogle comes up to him. She sees that he has Geostigma and tells Denzel that a man has told them that he's going to cure them. She then brings Denzel over to a pickup truck where a lot of kids are gathered; Denzel gets on. It turns out that the man the girl mentioned is Yazoo.
Cloud comes back to the Church and finds Tifa laying among the flowers; Marlene is nowhere to be seen. His Geostigma flares up and he sees visions of Sephiroth before blacking out. He awakens later to find himself and Tifa back in Seventh Heaven. It turns out that Reno and Rude have brought them there. Before leaving, the Turks tell Cloud that the children that he and Tifa were taking care of are now gone.
In the Forgotten City, Loz watches over Marlene as Kadaj examines the materia the former took from the church. Kadaj then takes a piece of materia and presses it into his arm.
By this time, night has fallen over Edge, and Tifa has awakened. Cloud tells her that Reno and Rude are out looking for the kids. Tifa in turn asks him if he has Geostigma. As they argue, Reno and Rude reappear. They tell Cloud and Tifa that they've learned that the children have been taken away to the Forgotten City.
Meanwhile, all of the children that Kadaj's gang has gathered stands before the lake where Aeris was laid to rest. From the other side of the lake, Loz keeps Marlene close while Kadaj addresses the children, telling them that they all have a special power from Mother that will help them fight against the Planet. He promises to cure them, then they'll all rejoin Mother and take revenge on the Planet. Kadaj then steps into the lake, letting out a dark-colored cloud. He drinks some of this tainted water then asks the children to follow his lead, which they do, including Denzel. After drinking the water, the kids' pupils narrow, making them look very much like the silver-haired men's eyes.
Cloud races to the Forgotten City on Fenrir, but is thrown into a sort of brightly-lit dream world along the way. He's back to back with Aeris, who asks why he's come. Cloud says he wants to be forgiven. Aeris lightly asks, "By who?" before the scene vanishes and Cloud finds himself being shot at by Yazoo and Loz. The children drop from the trees, forming a barrier between Cloud and the silver-haired men that Cloud manages to get through. Now surrounded by the puppet-like children, Cloud says he's here for the kids, but Kadaj claims he's a traitor to their mother. Marlene calls Cloud's name, catching Kadaj off-guard, and a battle commences. During this fight, a strange red shadow appears to help Cloud, who loses his cell phone in the lake.
After the fight, everyone is gone save for Cloud and Vincent. Vincent explains that Geostigma is caused by the body overworking itself to remove harmful influences—in other words, Jenova cells. He also mentions that Tseng and Elena had drifted to the Forgotten City, on the brink of death. He managed to save them, but he's not sure how well. From them, Vincent learned that they had come into possession of Jenova's head, and that if Kadaj and his gang got ahold of it, they could even remake Sephiroth. As Cloud and Vincent talk, they hear a rustling, and Marlene runs out. She starts to tell Cloud about Tifa, but he reassures her that Tifa's all right. Cloud asks Vincent to take Marlene back to Seventh Heaven, so that he can go see Rufus. Vincent doesn't approve of this plan, and Marlene is frustrated with Cloud. Cloud tells her to wait a little longer, and that the fight is about to start soon. Vincent gets the impression that there's more to this than meets the eye.
A brief flashback follows, where Cloud is back in Seventh Heaven with Tifa and the Turks. A similar scene had played out then, with Cloud asking the Turks to take care of the problem with the kids while he goes to talk to Rufus. At the time, Tifa accused Cloud of running away from his problems, while Reno tells him to go to the Forgotten City.
Back in the Forgotten Capital, troubled by what had befallen Aeris in the past, Cloud asks Vincent if sin can be forgiven. The gunman admits he's never tried it. Cloud then makes his decision; he'll take Marlene home, and try it for himself.
A scene follows of Cloud's cell phone as it descends to the bottom of the lake. A flurry of voice messages—from Reeve, Yuffie, Tifa, and others—can be heard.
In Edge, the Meteor memorial has been chained up by Yazoo and Loz, and is surrounded by their puppet children. All around them, people are protesting. Shadow Creepers are summoned to attack the people, and chaos breaks loose. In the middle of all this, Tifa arrives and spots Denzel; she tries to talk to him, but to no avail. Meanwhile, Yazoo and Loz are confronted by the Turks. Yazoo and Loz believe that Mother is inside the memorial, but the Turks are unable to verify this. Yazoo insults the two Turks, who move in to attack. In another part of the city, in an incomplete high-rise, Kadaj is with Rufus. They talk about what would happen if Kadaj gets Mother's cells, and Rufus says they'll stop him from carrying out Jenova's will. Kadaj asks, "Shall we end this?" then summons Bahamut-Sin, who comes to land before Tifa in the town square. Reno and Rude start to take off after seeing Bahamut-Sin, attempting to save some kids along the way, and Yazoo and Loz go after them. In the meantime, Bahamut-Sin destroys the memorial. Denzel has come to, but Tifa, who was protecting him, has collapsed. Barret, Nanaki, Cait Sith, Yuffie, Cid, and Vincent all arrive on the scene to fight the summon beast, as Tifa and Denzel watch from the sidelines. Cloud arrives and tells Tifa and Denzel that Marlene is safe at Seventh Heaven, and Denzel says he'll go back there and wait with her. Cloud and Tifa then join their friends in the fight.
Meanwhile, Rufus stands up from his wheelchair, tossing off his covering as he does so. In one hand he holds an oblong black box—Jenova—which he then tosses over the edge. A furious Kadaj lets out a blue fireball.
Back at the fight against Bahamut, Cloud's friends give him help as he rises upward to meet the monster—including some spiritual support from Aeris. Cloud defeats the summon beast, which falls and disappears.
Elsewhere, Rufus has fallen off of the under-contruction high-rise. He shoots toward Kadaj, causing an explosion; Kadaj then dives off himself, going after the box containing Mother. Kadaj manages to get in between Rufus and the box; Rufus continues shooting, hitting the box. Kadaj gets hold of the box, while Elena and Tseng appear out of nowhere to save Rufus. Kadaj lands on the ground; Reno, Rude, Yazoo, and Loz are there, and Cloud is on his way. The three silver-haired men see Cloud coming and take off on their bikes. As Reno and Rude go to meet Rufus, Cloud follows his foes onto an unfinished highway. As Kadaj takes an alternate route, Cloud finds himself up against Yazoo and Loz in a tunnel. Reno and Rude arrive at the other end of the tunnel, and after Cloud passes, they set bombs to take care of Yazoo and Loz. Cloud catches up with Kadaj, entering Midgar. As Kadaj races off, Cloud pauses to remove the cloth covering his left arm, revealing a Geostigma-scarred arm and a pink ribbon, before following his foe.
Kadaj arrives at the Sector 5 church and examines Jenova's box, only to find a huge tear in it. With all of Mother's liquified remains having leaked out, he's devastated. When Cloud arrives, Kadaj destroys a pillar and escapes to the rafters to attack Cloud with magic, but afterwards, something unexpected happens. Green bubbles rise out of the ground, followed by water, which rains over the interior of the church. As Kadaj fights against it, Cloud finds the water healing his Geostigma. Kadaj escapes, and Cloud follows, encouraged along by Aeris' voice.
At the Shinra Building, Kadaj begins his battle against Cloud. Meanwhile, Cid's airship, the Sierra, arrives on the scene. The whole party is on board, ready to fight alongside Cloud, but Vincent advises that they leave the two of them alone. As she watches the battle below, Tifa notes that Cloud has lost something in the two years since the final battle.
Down below, the fight continues, and Cloud has the upper edge. Kadaj, having lost his sword, is now hanging off the edge of the Shinra Building. The Jenova box is tossed out, when it comes apart, revealing dark green liquid spilling out. Having seen this, Kadaj leaps after the box and absorbs the liquid. Cloud leaps after him, but upon reaching him, Kadaj has transformed into Sephiroth, complete with Masamune. Sephiroth reveals his goal: to take control of the Planet and use it to travel to other worlds, as his Mother did before him. The final battle between Cloud and Sephiroth then commences, as darkness descends. Sephiroth pins Cloud with his masamune, wishing to send him spiraling into despair, but Cloud, armed with thoughts of his friends, fights back and uses all the multiple parts of his sword to defeat his nemesis in one final, ultimate attack. Defeated, Sephiroth sprouts a single black wing, says he won't become a memory, and transforms back into Kadaj. With his weapon back in his hand, Kadaj tries to attack Cloud, but he is too weak, landing in Cloud's arms instead. Aeris' voice calls out to Kadaj, and it starts to rain; Kadaj takes the voice to be that of his Mother. Kadaj reaches upwards, disintegrating into Lifestream particles.
Back in Edge, the rain cures the children outside of their Geostigma; it likewise cures Rufus, who sits in an alley with his four Turks, reunited again. The Sierra hovers over the Shinra Building in Midgar, and everyone on board is in a celebratory mood. Staring at the rain, Tifa silently thanks Aeris. Cloud looks up at the airship, feeling calm, when a shot penetrates his chest. Behind him, Yazoo and Loz have survived Reno and Rude's explosion and their left arms are now dotted with absorbed materia; they are also disintegrating. Cloud starts after them, when there's an explosion. In Edge, Marlene and Denzel watch the rain fall from inside Seventh Heaven.
Cloud is laying in a white field, when Aeris hand comes to rest on his forehead. Cloud says, "Mother", and Aeris scolds him. Another voice—Zack's—converses with Aeris. Cloud then awakens to find himself floating in a large pond that has formed in the Sector 5 church; he is surrounded by children. One of the girls tells him that "sister" told them all to come here. Along with the kids, there are a number of other people present, including the Sierra's passengers, Marlene, and Denzel. Nanaki says there are still kids with Geostigma, and indicates Denzel. Cloud holds out his hand to him, and Denzel is lifted into the water. Cloud pours water from his hands over Denzel, who is then cured. Everyone present celebrates. Then, at the front of the church, Cloud sees Aeris kneeling before some kids. She stands up and heads to the door, where Zack is waiting. She turns to look at Cloud, seeing that he's all right, then leaves. Zack waves goodbye, and follows her out of the church, into the bright light beyond.
Written by Reeve, September 2005.