Well there are 2 stories in CoM, Sora's and R/R (Riku's story), In Sora's story, the only confirmed unknown that was killed was Vixen, supposedly for releasing too much imformation to Sora or something, so Axel he his way and kill him/she/it. In CoM you only see 7 of the unknowns, not including the DiZ (who we dont know if he's ranked in the organization), you see the EM (at least I think its him because his face is not known but it could be zexion, he wouldn't count), Axel, Larxene, Lexeaus (sp?), Zexion, Vixen and Marluxia (Final boss in Sora's story).
Through out the story, Sora begins to forget his memories every level he goes up, but by losing those memories important to him (like memories of Kairi), hidden memories begin to surface, like ones of a mysterious girl who once lived at destiny island with them.
It appears that this girl is being help against her will by the organization, and she is trying to get through to Sora through his memories, she seems inocent, but to be she seems like she's trying to hide something, like she's pretending to be apart of Sora's memories so that he can forget something important, I don't think she was really there, but I think that at some point she realized what she was doing and tried to stop it, Finally when Sora meets her she sends him away in that weird flower thing, saying that he won't remember anything about castle oblivion and her (something along those lines), and with that he is put in to what apears to be some deep slumber, setting the stage for kh2. As for R/R I haven't quite gotten there but i'll keep you posted if you want.