In Chain of Memories, all Organization XIII members except for Axel are killed.

Sora kills Larxene.
Axel kills Vexen, who was weakened by Sora.
Sora kills Marluxia.
Riku kills Lexaeus.
Replica Riku kills Zexion (or absorbs Zexion, or whatever happened there).

Sora does beat Axel, but Axel escapes before Sora can kill him. You know this because Axel leads Replica Riku around in Riku's story, and some of that happens after Sora kills Marluxia.