In the E3 trailer of Halo on Xbox One, we saw Master Chief walking through a desert (cloaked) until he stumbles upon an awakening Guardian. He pulls out the chip Cortana used to live in and his face is revealed by a shock wave emitted by the Guardian. As epic as it is, we all are wondering," where are they?"
Warning: while this isn’t considered a “Spoilers” it could contain some spoiler-like content, so I really advise that you take precaution before reading more.
A lot of people have suggested that the place where the Master Chief and the Guardian are is the Ark, which for had been for some time now revealed to be the setting of Halo Wars 2, which is also involved in this theory. Something I’d like to also point out is how the Domain is always described as a system that spans the known galaxy, and as established in Halo 3: the Ark is just a couple of light-years beyond the rim, considerably far enough to be beyond the reach of the Domain’s control. This implies any Guardian possibly still resting on the Ark was not able to receive the call by Cortana.
As for a Guardian being on the Ark to begin with: we do not have that much lore to give many historical theories as to why it could be there, but I have a theory that derives from Halo Wars 2, and could possibly come into play in its story. In the Beta, one of the maps is described as (not the precise wording) “A scarred land by an awakened giant” many of us are familiar with that particular kind of destruction from Halo 5 Guardians.
Its importance to the Master Chief: you can check out on a different topic of mine “No Cortana!” I suggested there’s someone else who could be controlling Cortana, a majority of people including myself think that this could be true. If so, then I also think there is a possibility that she could return, I think her AI matrix could be extracted from the Domain and placed back into Chief’s chip, which he holds in the E3 trailer, and would also reveal the one who may be really behind this. Chief could try to use the Guardian to return to the Domain (since the gateway on Genesis has likely been shot off) and rescue her.
Conflict: though I have not watched the video, I know Halofollower has made a video suggesting that the Banished might be in Halo 6, which would provide an enemy to fill in the roll of the Covenant as well as a conflict for Chief on the Ark.
How does Chief know: Halo Wars 2 could again be involved with this, but if not, its possible Mendicant Bias could still be out for atonement, and tries to contact Chief similar to how Cortana contacted him in Halo 5. Taking control of the Guardian himself, Chief and him return to the Domain, rescue Cortana, and finish the fight!