Advent Children is set two years after the events of the classic role-playing game Final Fantasy VII, which revolved around the antagonist Sephiroth's attempt to absorb the Lifestream, the essential essence of the Planet, in order to be reborn as a deity. Despite being thwarted by Cloud Strife and his allies, the catastrophic spell known as Meteor devastated the city of Midgar and left a lasting impact on the world.
In this sequel, the remnants of Midgar have given rise to a new city named Edge, where Cloud and his childhood friend Tifa Lockhart now run a courier service. They also care for Denzel, an orphan burdened with the mysterious and debilitating illness called Geostigma, as well as Marlene, the adopted daughter of Barret Wallace. Cloud, haunted by his failure to protect Aerith Gainsborough, seeks solitude, distancing himself from both his friends and responsibilities.
The plot thickens when Cloud receives a summons from the seemingly resurrected former president of the Shinra Company, Rufus Shinra, who requests his assistance in vanquishing Kadaj, Loz, and Yazoo—three beings that represent the remaining essence of Sephiroth. Determined to revive their master using the remains of the infamous extraterrestrial entity, Jenova, Cloud initially refuses and leaves the meeting.
However, the situation escalates as Kadaj and his companions manipulate children affected by Geostigma, leading Denzel to fall into their deceptive promises of a potential cure. Meanwhile, Loz pursues Tifa and Marlene to Aerith's church, where a confrontation occurs, resulting in Tifa's unconsciousness and Marlene's abduction. The children are subsequently taken to the ruins of the Forgotten City, where Kadaj proclaims his goal to unite them with Jenova.
In a tense rescue attempt, Cloud arrives but is overwhelmed by Kadaj's group until his old ally Vincent Valentine intervenes. Afterwards, Cloud returns to Edge to confront a more substantial threat, as Kadaj summons the terrifying Bahamut SIN and other creatures to wreak havoc. With the aid of his companions, Cloud fights valiantly and defeats these monstrous foes.
In a dramatic twist involving Jenova, Kadaj confronts Rufus, who possesses its remains. As Kadaj attempts to seize this power, a confrontation ensues, leading to an explosive showdown where Reno and Rude thwart Kadaj's plans. The ultimate battle occurs between Cloud and Kadaj, escalating into a fierce struggle where Kadaj merges with Jenova's remains to become Sephiroth. As they clash, Sephiroth, having the advantage, pierces Cloud’s shoulder and taunts him about taking away his most cherished memories. In a moment of determination, Cloud responds that he treasures everything, leading him to unleash his powerful Limit Break, Omnislash Ver. 5, ultimately defeating Sephiroth.
In the aftermath, as Sephiroth’s spirit departs, a dying Kadaj is cradled in Cloud’s arms, during which a miraculous healing rain begins to fall over the land, curing the afflicted of Geostigma. The story concludes with a vision of Aerith and Zack Fair, who reassure Cloud that it is not his time to join them. Rejuvenated and surrounded by friends, Cloud experiences a sense of connection and companionship that he thought lost. As he celebrates with the rescued children bathing in the healing rain, a scene during the credits shows him riding his motorcycle into the unknown. In Advent Children Complete, an additional post-credit moment reveals Zack's Buster Sword within Aerith's church, surrounded by flowers, symbolizing a profound connection between the characters and the sacrifices they made.