They Were Once Organization XIII

And now quite a few of them are dead.  Or in parallel universes.  Or in exile. 

Vexen: He's in a parallel universe now.  He got out before Xehanort could either A) Make him make more Replicas or B) Kill him. 

"How easy is it to corridor between the different universes?" --Aaand, Onto Another Universe

Lexaeus: Killed in Hollow Bastion Castle. He was an unfortunate victim of Xehanort.  He was captured and the Xehanort drove a blade through him. *mutters bad words about Xehanort*

"I did not go down without a fight." --A Date With Fate

Zexion: He's alive.  Xigbar didn't have the heart to kill him.  He let Zexion go, claiming he couldn't shoot the boy "Ienzo."  He now owns a bookshop in Hollow Bastion.

"Ienzo, I go by Ienzo now." –A Forgotten Remnant

Xaldin: Killed in the Keyblade Graveyard/Badlands.  Riku shoved one of his own lances through his gut and Sora landed a finisher on his head.

"Such use of power will easily backfire here." --Old Friends, Old Rivals

Marluxia: Unfortunately still alive.  He'll probably come back and cause trouble later.  However, Axel's sent him someplace unpleasant in the meantime.

"So quick to anger..." –Up Down Adventure

Larxene: Also unfortunately still alive.  She will come back and cause trouble later. But, before she does, she's got to get away from all the water.

"I am going to pick you off one-by-one!” –Larxene the Ruthless

Xigbar: Still alive.  Roxas probably would have killed him if he'd stayed around, but he didn't.  He'll be back to cause trouble later.

"I gonna take a rain-check on this battle.  See ya, Kiddo!"  --Final Match

Saix: Killed in Castle Oblivion.  He tried to kill Xehanort with darkness but failed.  The darkness backfired on him and he was consumed. 

"Remember me as I was, before I messed up." --Final Match

Xehanort: Killed in Castle Oblivion by way of 8 Keyblades full of light as well as an additional light-attack from Namine for good measure. 

"Four masters in one place... all fighting for the same side..."  --Final Match

Demyx (Now Demetrius): Alive and well, started his own band and travels around with Luxord as his business manager. 

"Come one, come all, come see the amazing Demetrius!" --Fantasia alla Marcia

Luxord: Also alive and well.  He travels around with Demy as his business manager.  But he is always up for a good game of cards.

"Perhaps a game of cards?" --Fantasia alla marcia

Axel: Well, I'd hope he's still alive.  He's got a few more battle scars thanks to Saix, but he's alive.  *SPOILERS* He'll stay alive.

"You don’t want to fight me, I’m not worth the effort.” –Struggle Away

Roxas: He's quite alive and quite happy.  It's his new mission to go out to the worlds and keep the balance of light and darkness, and become a Keyblade master while he's at it.

"Maybe me and Xion still want to do a bonfire!" –Friends Forever

Xion: She, like Roxas and Axel, is also still alive.  She's going to stick by her friends forever if she has any say about it.  Her new mission is to achieve the rank of Master.

"Shh, I like using magic." –Friends Forever