Okay, we know that the game is set post Halo 5 per the community update and in a gamespot interview F O Connor went into some detail about how the Banished pre date the Covenant and that Atriox is on the Ark trying to gain power. The Spirit of Fire lands with no idea if humanity has lost the war and tries to regain contact with the galaxy.
So this tells us a few things.
1 - Atriox and his Covenant do not seem to be aligned with the Created. This is simply by right of them having their own agenda to create a new empire and a history pre dating Halo 5. In fact I would even guess that with him and the bulk of his army on the Ark he is himself unaware that Cortana has, more or less, made a pretty good stab at conquering the galaxy.
2 - Obviously the SoF crew are unaware of this as well and really want to get back home.
Okay, I think that Cortana has a huge army of Prometheans on the other side of the portal at New Mombasa and, presumably, the Ark like the Halo Arrays is cut off from the Domain and controlled by a Monitor. She can’t get there yet, but needs to if whatever she has planned for the Halo arrays in Halo 6 is going to happen. So, they could play around with the idea that the Spirit of Fires crew are tricked into allowing Cortana to gain access to the Ark and open the portal for her forces. It could even be that this is how the SoF intends to escape.
I think that Atriox and his Covenant will fill a role similar to that of the Covenant in Halo CE as the early game antagonists but not the principal galactic threat. The stakes will get raised when the SoF learns that Cortana intends to take over the Ark and gain access to the Halo arrays. I then think the rest of the human campaign will focus on either blowing up or severely damaging the Ark to prevent her gaining access to control of the rings.
On the other hand…
If, and I sincerely hope its the case. We’re getting a campaign for each playable faction (because we all like nice things). It could be that the SoF focus is on escaping the Ark once this occurs although they may still make an effort to sabotage Cortana’s efforts. So that a bit like those 4 easter egg Scrin missions in C&C we spend the game as the Prometheans destroying the Banished on the Ark. I also suspect that the Covenant campaign might be Rtas Vadam on the Shadow of Intent. Which would be awesome but I am not sure how it would fit into the story.
Cortana gaining control of the Ark would make sense since it would be a nice bit of set up for Halo 6 and I’d be very surprised if they did something like have the big return of the Flood in a spin off game. Plus if they are in I am hugely surprised that they haven’t already teased them as a playable faction at E3. I mean the Prometheans I can kind of understand for various reasons although teasing any third faction would be a good marketing ploy IMO. Although a forth, well, we all like nice things.