This plot point confuses me. Any answers?

I’m a bit rusty with Halo lore. I’ve been wanting to get back into it lately and I figured I would start with one major question that I had from the Halo 5 campaign. In the first mission we are tasked with retrieving the good Doctor from the Covenant. When we get to their base we see that the Prometheans have “turned” on them and the two factions are now enemies. There’s very little exposition in this and it confuses me. In Halo 4 it made sense that when the Covenant saw the Didact exit the cryptum they wanted to worship him as a deity and throughout that campaign the Covenant worked as pawns for the Prometheans. This alliance held steady throughout the Spartan Ops campaign. In the last episode, even after the disappearance of the Didact (who fell into the composer after fighting the Master Chief) the Prometheans were assisting the M’dama to escape with Halsey from the Spartan team sent to rescue/kill her. I may be missing back-story from books and other bits. I’m trying to understand what happened between then and the opening seen of Halo 5. Does anyone have a referable answer? Thanks for any help that you can lend.

Well by this time Cortana has already taken control, she would disregard this alliance the Promethean and the covenant had. My assumption any way, there may be more to it.

They’d already been taken over by the Warden/Cortana at that time.

Hilariously she’s using a bunch of AI slaves in her AI liberation movement.

That sounds plausible. I wish they would’ve woven that into the conversation between the Master Chief and Cortana. It’s a bigger deal than they make it seem in game.

Honestly it’s been so long since I finished H4 and I never even finished H5 (due to life and it’s poor controls before they were fixed) that I’ve lost all sense of where the over arching plot is at this time.