Real Organization XIII

The real Organization XIII (真のXIII機関), also known as the thirteen seekers of darkness (13人の闇の探求者) or simply Organization XIII or the Organization, is a group consisting of thirteen different incarnations of Master Xehanort who seek to reforge the χ-blade and unlock the original Kingdom Hearts to remake the world. They serve as the final antagonists of the Dark Seeker Saga.

The true purpose of the original Organization XIII led by Xemnas was for each of the Nobody members to host a fragment of Master Xehanort's heart, turning them into clones of Xehanort, but the members' unforeseen independence made this goal impossible to realize. However, in anticipation of this failure, Master Xehanort had arranged to send Ansem, Seeker of Darkness back in time to his youth, to meet Young Xehanort and become a portal, travelling to different periods of time and gathering different incarnations of Xehanort who would be added to the ranks of a new Organization.

Due to the time travelling nature of many of the hearts comprising the Organization, future members first appeared in Kingdom Hearts with at least one making an appearance in every game since. As a group, it was first alluded to by Yen Sid in Signs of What's Next when he claims that one Keyblade Master will not be enough to counter what is "not a single one of Xehanort", before making its official introduction in Kingdom Hearts 3D: Dream Drop Distance.

Unlike the original Organization XIII, the real Organization XIII is not composed exclusively of Nobodies; some of the members are complete people, while others are time travelling hearts hosted within Replica bodies. Despite full knowledge of the purpose of this new Organization, many members use it as a means to fulfil their own independent goals, rather than out of loyalty to Xehanort.

Before Kingdom Hearts Birth by Sleep
Young Xehanort is visited by his future self's Heartless Ansem, Seeker of Darkness and told of the great plans Master Xehanort has in store. Given his task, but limited by the rules of time travel, Xehanort leaves his body behind and journeys into the future to make contact with the right hearts needed for the backup Organization.

Between Kingdom Hearts Birth by Sleep and Kingdom Hearts coded
Unable to physically interact with the world without a body to reside in, Young Xehanort acquires one in the form of Even's newly created Replicas and begins his mission. He recruits Terra-Xehanort and Vanitas, whose heart is incomplete, bringing their hearts into the future.

During the time Ansem exists within Riku's body, Young Xehanort recruits him into the new Organization, bringing his heart into the future.

During Sora's journey through Castle Oblivion the brainwashed Riku Replica, believing himself to be the real Riku, is recruited by Young Xehanort. During this time Vexen is eradicated by Axel.

Early in the life of the unique Replica Xion, before any real personality had taken shape, Young Xehanort recruits her into the Organization, bringing her heart into the future.

After their respective defeats at the hands of Sora, the recompleted Elrena and Lauriam accept Young Xehanort's offer to return to being Nobodies, and are each made host to part of Xehanort's heart as Larxene and Marluxia once again.

After their defeat, Demyx and Luxord are recompleted as humans. Accepting Young Xehanort's offer, they return to being Nobodies and rejoin the Organization. At some point prior to his final defeat and recompletion as Master Xehanort, Xemnas's heart is collected by Young Xehanort so he can be made a member of the real Organization.

Kingdom Hearts coded
With the demise of Ansem and Xemnas, the original Master Xehanort is recompleted and assumes leadership of the newly formed Organization. The body of Terra is also recompleted, but his heart remains bound within Xehanort's guardian.

Young Xehanort visits Radiant Garden where he recruits the recompleted Braig and Isa, returning them to their Nobodies Xigbar and Saïx and making each host to part of Xehanort's heart.

Kingdom Hearts 3D: Dream Drop Distance
Ansem and Xemnas are both given Replica bodies to inhabit. Riku Replica's heart is put into a Replica body, becoming Dark Riku. While he briefly accompanies Young Xehanort without a body, Vanitas is soon given his own Replica body to inhabit. Terra-Xehanort's heart makes Terra's recompleted body his vessel.

Young Xehanort succeeds in filling twelve of the Organization's seats. Vexen and Demyx are not considered suitable for the final roster, leaving the Organization one member short. Xehanort attempts to make Sora into the final vessel, but when Sora is rescued by Riku, Mickey, and company, the Organization disperses to their proper times, while Master Xehanort remains confident that in time he will complete his Organization.

Members
By the time the real Organization XIII is ready to re-enact the Keyblade War they are composed of thirteen active members, with two additional members serving as reserves. Additionally, Vexen creates twelve newer Replicas from each of the active members of the Organization save Master Xehanort himself, to replenish their ranks should the need arise.