Organization XIII is an elite team of 13 nobodies. it's only the reguler nobodies that are in service to the villain leage, but however, the reguler nobodies had not yet appeared themselves. they will not be with the Villain leage, cause of them being Enemies of Maleficent, but their minions, the Nobodies, cause of Fagin, may be in service to the villain leage. though why Fagin has been able to control regular nobodies is because the Elite ones are long defeated by Boy Sora. Though, it's interesting that currently known survivers like Xemnas, Xigbar, Saix, and formerly Xaldin, have been in leage service. The one surviver that didn't is Axel, and he has a mysterious plan concerning the supposingly "desised" members of the Organisation.
In Spirited Away/KH 3D, the resurrected Master Xehanort reforms Organization XIII, only consisting of several incarnations of himself from many alternate timelines. So far only known members are Master Xehanort himself, Xemnas, Ansem, Seeker of Darkness, Young Xehanort, Braig, and Isa. There are also six others whose identities are not yet revealed. Sora was supposed to be a member, but Lea saved him from being possessed by Xehanort. Master Xehanort says that someday a new Organization, which he calls 13 Hearts of Darkness, is supposed to fight against the 7 lights. The Organization soon vanished into darkness after Sora was saved.
Young Xehanort explains to Riku that they originally wanted him to be their 13th Vessel but because he has built an immunity against the darkness, like the Keyblade they chose Sora instead.
Master Xehanort mentioned that 1 of the 7 lights was in his possession - this, given that he merged with Terra, is presumably his heart, as Ventus's remains in Sora and Aqua is trapped in the Realm of Darkness.
Other former Organization members like Ienzo, Aeleus, Even, and Dilan appeared in Radiant Garden in Ansem's study during certain cutscenes. However, the fates of Demyx, Luxord, Marluxia, and Larxene currently remain unknown.
Xemnas explains that the nature of a Nobody is to gain a heart quickly after losing it. As such he states the true purpose of Kingdom Hearts was to prepare it's members to be vessels of Xehanort.