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 for Young Xehanort to be sent by Ansem, Seeker of Darkness to travel to different periods of time and gather different incarnations of Xehanort, who would be added to the ranks of a new Organization. Young Xehanort succeeds in filling twelve of the Organization's seats, and he and the revived Master Xehanort attempt to make Sora into the final vessel. When Sora is rescued by Riku, Mickey, and company, the eleven members aside from Master Xehanort begin to fade away back to their proper times, but Master Xehanort remains confident that in time he will complete his Organization and continue his plans.
There are currently twelve seen members of the true Organization XIII, but only six have been named so far.
- Master Xehanort: The original Xehanort and the mastermind behind all of his incarnations' actions.
- Young Xehanort: Master Xehanort in his youth, who traveled through time with the assistance of Ansem.
- Ansem, Seeker of Darkness: Terra-Xehanort's Heartless.
- Xemnas: Terra-Xehanort's Nobody and the leader of the first Organization XIII.
- Xigbar: Braig's Nobody and a member of the first Organization XIII.
- Saïx: Isa's Nobody and a member of the first Organization XIII.