In preparation for the coming of the second Keyblade War, Master Xehanort brought Vexen into the Organization to gain access to his Replica Program, setting aside twelve of the twenty known replicas for the members of the Organization. When each member of the Organization was defeated during the Second Keyblade War, the empty vessels left behind transformed into the Replica Xehanorts.
When Sora, Donald, and Goofy entered Scala ad Caelum, the Replica Xehanorts attacked them before Master Xehanort absorbs the replicas to increase his powers, transforming themselves into armor that Master Xehanort uses for his final battle.
After Sora shatters Master Xehanort's armor, the Replica Xehanorts are sent to battle the remaining Guardians of Light at the Keyblade Graveyard. They successfully trap all but Mickey in a dark void. All twelve Replica Xehanorts are held off by Mickey (and by a future Sora) before he frees the other Guardians from the void.
In a last ditch attempt to stop the Guardians of Light, the Replica Xehanorts merge into one copy of Armored Xehanort, who fight the future Sora and a revived Kairi. Despite their strength, the Replica Xehanorts are weakened enough by Sora and Kairi to be finished off for good by all the Guardians of Light, ending the threat of Xehanort for good.
- Originally believed to be phantoms of the original Xehanort, the Replica Xehanorts are shown to have the individual powers of each member of the real Organization XIII.