This might not be a popular opinion, but I think it would be a fantastic way to introduce a third faction. I'd like to see Atriox square off against Prometheans or Flood. Only issue with this is that it might not make sense for him to be fighting Prometheans. My theory is that he's working/fighting for the Created. So I don't know.
But if I had to choose I'd probably choose what he was doing on the Ark before the Spirit showed up.