I. XemnasDefeated by Sora and Riku at the end of Kingdom Hearts II. He was trying to dispose of the only threat standing between him and Kingdom Hearts. Disappeared in Darkness in what appears to be a black variation of the white Nobody thorns. He was the thirteenth and final member to fall, but since both his Heartless and Nobody have been slain, Master Xehanort is now able to return from the darkness.
II. XigbarDefeated by Sora, Donald, and Goofy in the Hall of Empty Melodies in The World That Never Was. He started the fight to try to prevent Sora and company from ascending any farther up the castle but disappeared into Darkness. He was the ninth member to disappear. He was later recreated as Braig, but becomes Xigbar.
III. XaldinDefeated by Sora, Donald, Goofy, and Beast at Beast's Castle. He was on a mission to turn the Beast into a Heartless and Nobody. Disappeared into Darkness and wind. Xaldin was the seventh member subject to elimination. Due his elimination, he was revived as Dilan.
IV. VexenDefeated by Axel as a way to gain Marluxia's trust. Vexen opposed Marluxia's plot and Marluxia wanted him eliminated. Disappeared by incineration into Darkness. He was the first member to fall. His death lead to the recreation of Even
V. LexaeusDefeated by Riku while possessed by Ansem, Seeker of Darkness. He was trying to make Riku use the Darkness inside him. From what is shown in the cutscene of his elimination, he was helpless against Ansem, Seeker of Darkness due to his weakened condition after his brutal fight with Riku. He disappeared into Darkness, and was the third member eliminated. His death led to the reconstruction of his original persona, Aeleus
VI. ZexionDefeated by Riku Replica and Axel. Axel wanted no evidence of his actions in Castle Oblivion, so when Zexion was extremely weary from his battle with the real Riku, Axel had the Riku Replica absorb Zexion. He disappeared into gaseous Darkness while engulfed in the Replica's energy. Zexion was the fifth member to fall. His death lead to Ienzo's recreation.
VII. SaïxDefeated by Sora, Donald, and Goofy. He was confronted simply to try to eliminate the last of the Organization. He disappeared into gaseous Darkness. He was the eleventh to be defeated. He was later reborn as Isa.
VIII. AxelEliminated in a sacrificial attack to save Sora from an army of Dusks. Similar to a fire, he seemed to "burn out" into Darkness, resembling ashes. Axel was the eighth member to fall. He was later revived as Lea.
IX. DemyxDefeated, by Sora, Donald, and Goofy. He was one of the few mentionable people destroyed in the Battle of the 1000 Heartless. He confronted Sora and company just for the sake of battling in the war. He disappeared into Darkness and appeared to have boiled up and evaporated. He was the sixth member to disappear.
X. LuxordDefeated by Sora. He captured Donald, Goofy, Riku, and Kairi, forcing Sora into one of Luxord's "games." Sora was able to beat him by "winning the game" and slashing through his shield of cards. He disappeared into gaseous Darkness. Luxord was the tenth member to be eliminated.
XI. MarluxiaDefeated by Sora. He was trying to destroy Sora since he couldn't control him. Marluxia himself is never actually fought, but after Sora destroys a clone, a machine-like Nobody and an angel-like, feminine reaper, all Marluxia's energy is gone and he is beaten. He disappeared attempting to grab Sora in gaseous Darkness in a flurry of flower petals. Marluxia was the fourth member to disappear.
XII. LarxeneDefeated by Sora, Donald, and Goofy. She was on a mission to kill Sora after her plan fell apart. She would have succeeded, but an attempt to save Sora by Naminé, Donald, and Goofy gave him the strength to fight back, and Larxene eventually met her end. She disappeared into Darkness. Larxene was the second member to fall.
XIII. RoxasArguably the only surviving member. Roxas permanently sealed himself within Sora just before the final battle with Xemnas, willingly giving up his physical existence. Although he is not gone, he was the twelfth member to "fall".
XIV. XionWhile technically not an official member, she was still part of the Organization for a while. She was defeated by Roxas while battling him and then faded away to join with Sora. If she was considered a member, she would be the sixth to be defeated.