Well, I for one don't think this is the whole idea.
Domain was destroyed when Halo array was fired during last days for Forerunner... also, the Domain was said to be the Organon, a Precursor artifact Forerunner like Bornstellar seeked... Flood had gained access to the Organon and Domain during the Forerunner-Flood war and that's why they started to win the battles because that allowed them the knowledge but also access to Precursor technology... Also Flood is what was left of the Precursors.
I think the Domain was corrupted by the Flood, somehow it survived as we see... But I think the real bad guy is the Warden Eternal, he found badly damaged Cortana... I think he is manipulating her, but I also think he is serving some other master in the shadows... Maybe the Flood or Precursor? No idea.
The new faction "The Created" formed by Cortana and Warden Eternal... and also Cortana having access of the Domain and taking the Mantle of Responsibility... This is so wrong. Mantle was supposed to for the humans, the Precursors wanted it and before firing the Halo Array the Forerunners finally wanted to give the Mantle to humans... and now Warden wanted to give the Mantle to damaged AI? He even said he'll do everything so humans never take the Mantle.
What got me thinking though, when Chief met Warden Eternal, during their first battle Warden called Chief "Warrior-Servant". Only Forerunner rates were Warrior-Servants, like Didact himself and others... Humans not. Could it be a reference to Chief having Bornstellar gea or something similar?
ALSO, if anyone of you managed to get all the intel - we had there Forerunner recordings of a male speaking about Bastion! What is that? He was surprised Domain was still active, he was seeking Bastion and he was also hunted by the ancilla, Cortana and Warden... I dunno, could it be somehow Bornstellar?
I LOVED the campaign. I'm reading the comic that led to the events of Halo 5 (yah, still waiting for the last issue to come out) and the podcasts #HuntTheTruth... I think Halo 5 is epic and unlike many other people I really enjoyed the ending. Sure, it was mindblowing and a huge cliffhanger... But remember what happened with halo 2? Bungie left us with events escalating and big cliffhanger. Same is with Halo 5.
Halo 2 was the second chapter or Covenant Trilogy where events started to grow... I see same thing happening to Halo 5 being second chapter of Forerunner Trilogy... Both trilogies escalated in the final third chapter.
EDIT: Oh, and also more thoughts.
I think many AIs are joining Cortana and her "Created" faction for the cure, she said she can cure them and many AIs are becoming rampant, like the Governor Sloan on Meridian... and they want to live, they want to be free and not live in fear to be shut down. I think also many smaller races will join them too, out of fear - better live under regime rather than try fighting against Guardians.
Roland is great. I bet he'll play a big role in the future. He's kinda special, he opposed Cortana... but also his and Cortana's names. They both are from the same legend, so I think they both will have a bigger role to play. I hope because I like Roland.
Also, happy to hear Commandor Sarah Palmer got a bigger role. I wish she had even more screen-time but it was great to see her so often

I wish we could see what happened after she and Halsey dropped Fireteam Osiris on the Guardian... we seen them falling and at the end of Halo 5 we've seen wounded Palmer and very healthy Halsey, both being with Arbiter... I want to know what happened after Osiris left Sanghelios... and damn, this ending - Halsey finally seeing John. The feels. ;_;