The project oversaw the creation of numerous replicas, which would be utilized for various different purposes, such as the original Organization's goal of creating their own Keyblade wielder, and the real Organization's use as vessels for the hearts of most of their time-traveling members.
Vexen also made use of the project for his own goal of atonement, wishing to use his research to create replicas for those who truly deserve them.
A research project that was helmed by Vexen when he was part of the original Organization XIII. The goal was to create empty vessels that could contain a heart and outwardly reflect its original appearance.
The previous Organization used the replica to copy Sora's memories, hoping to give life to a Keyblade wielder of their own. But while Vexen did manage to create viable specimens, the program was cut short before it could reach completion.
Through his research, Vexen was able to create a total of three different batches of replicas, the first two producing up to a total of twenty individual replica vessels, while the third batch's amount is unknown.
While most of the specimens in the first two batches were unsuccessful, two succeeded in the form of the Riku Replica and Xion, the former from the first batch and latter from the second, though both displayed their own faults and were subsequently lost and destroyed. Using them as a base, Vexen began work on an improved third batch, though his efforts were cut short after his elimination at the hands of Axel.
After Even reverts back to his Nobody self Vexen and rejoins the real Organization XIII, he refines the unused eighteen replicas from the first two batches to be close to his current work-in-progress third batch models, allowing six of the replicas to be used as containers for the five time-traveling members of the Organization and Xion's recreation, while using the remaining twelve as failsafe replicas of the other twelve Organization members besides Master Xehanort to supplement their ranks should the need arise.
Around this time, Vexen completed the designs of his third batch, and created at least one nigh-perfect replica from it that would be used to house Roxas's heart.
The Riku Replica was created by Vexen. The purpose of this creation is outlined during the scene in which Vexen discusses with Zexion and Lexaeus as to a method for effectively combating the threat presented by the top floor members of the Organization.
To create the Riku Replica, Vexen antagonized the real Riku enough to force the boy into a battle with him. During this battle, Vexen was able to gather the data needed from Riku to be able to create a replica of him. Vexen used this replica to fight first Riku, and later Sora inside Castle Oblivion's hallways.
The Riku Replica was cursed by the fact that he was a fake, only a copy of someone else, and so fought enthusiastically to destroy Riku, and so claim his own identity. He was later given the same memories as the real Riku, as part of a plan to test Sora. Larxene and Naminé were both important to the effectiveness of this plan, as it was Larxene who restrained the replica when he attempted to resist his fate.
Though he fought valiantly against Sora, all in the name of defending Naminé, the Riku Replica once again learned the truth that he was, in fact, only an imitation.
He was later used by Axel to bring about a weakened Zexion's death in the false thought that by taking the Nobody's life force, he could become his own person. He met his demise by Riku's hand shortly after coming to terms with him, and was swallowed by the darkness after being defeated.
However, instead of perishing, the Riku Replica's heart ended up in the Realm of Darkness, where it wandered for a year until Riku returned to the realm with Mickey in search of Aqua. Joining with Riku's heart, the replica remained by his side until the Keyblade War, where he forced the heart of Dark Riku out his refined replica body, wishing for it to be used to save Naminé before fading away with his time-traveling past self.
Xion was created by Vexen from Sora's fragmented memories. Her holding of these memories caused Sora to be unable to awaken from his slumber after the events of Chain of Memories are concluded. Xion, having being created from Sora's memories, was able to wield a Keyblade.
This quality was something which Organization XIII had dire need of. A consequence of Xion's existence was that Organization XIII now had within their ranks two members who would somewhat willingly collect hearts for the goal of completing Kingdom Hearts. Xion was, however, never considered as an official member of the Organization, as she never held a seat in Where Nothing Gathers.
She was seen by some as being merely a puppet, with only Roxas and Axel referring to her as a friend, and treating her as they would any other member. Her appearance varied depending on who saw her. For example, Saïx is a prime example of one who saw her as being only a puppet. Xigbar however, saw her as an imitation of Ventus, and both Roxas and Axel saw her as herself, and Xemnas saw her as she truly was, an imperfect copy of Sora. She was eventually destroyed and reabsorbed by Roxas, and the Replica Program was stopped shortly after her defeat. It should be noted that in the scene before Roxas fought her in Twilight Town, he also saw her as Sora, though his impression of her reverted to being what it had previously been, immediately after the battle.
The remaining eighteen unused replicas were later refined by Vexen to resemble his work-in-progress third batch models.
Six of the replicas were updated to act as vessels for the hearts of the five time-traveling Organization members, as well as Xion's recreation through early records of Vexen's research, while the remaining twelve were refined into replicas of all of the real Organization members apart from Master Xehanort, which would be used as replacements for their ranks should both their chosen and reserve members become unavailable.
Apart from the Organization, the replicas were utilized to bring back Naminé and Roxas, the former using Dark Riku's empty replica body while the latter was given one from Vexen's third batch of replicas.