Zexion and Axel don't get along too well. Then again, how many characters actually like Axel? Anyway, Axel clearly doesn't give a damn about Number VI especially after he gets beaten by Riku. Axel manipulates Riku Replica into thinking that he can become a real person if he becomes strong, and tells him that Zexion is a great place to start. Therefore poor Zexion meets his end by being absorbed into a clone.