Plot spoilers will be tagged.
Phases end when Overlord gets to 1HP and starts its next turn.
The Omega mission is the final mission before end credits and New Game+.
For a "how to beat" or "best strategy" guide, go to the Fight with overlord (SPOILERS) discussion.

People in the Discussions mention a certain betrayal by Rassa (Crimson Pact & Ragnarok) like it's the default, but I didn't experience it. Things played out entirely in my favor after the endboss, so I'm guessing reputation plays a hand along with the choices you've made up to that point.

I beat the endboss with a lvl27 party of Void Psyker, Prototype, Hacker, and Smuggler. Yes, it was stressful. No, my first attempt failed. Just plan for the battle and see how it plays out.

Only way to hurt Overlord is to damage any of its 4 Printers, which will finish self-printing/spawning an enemy in very few turns. Only way to get another Printer is to defeat the enemy it printed. As you defeat the Printers, their starting HP will lower and eventually only a single Printer will spawn.

Attacking Overlord will heal its Chemical, Void, Nanite, and Fire Cannons, but will[?] still harm it. Be mindful of Overlord's non-explicit elemental immunities.

Beyond its 6+ shields, Overlord can be directly harmed without worry.
Its 2 Gargantuan Claws, which lack shields, will either grab-stun an ally with its crushing grip (doing damage every turn until *somewhere above 2000* damage is inflicted on the claw) or attack. Pretty sure the left is strictly the "grab" one and the right is the "attack" one.

1. Loot everything before descending the stairs to the North. You might get better equipment.
   
2. Your favorite flying drone should be down the hall on your right before proceeding towards the boss, which should be the only fight on this mission btw.
   2a) Help it out if you want an ally during the battle who'll make Phase One hella easier, Phase Two a bit more stressful, and might not make it to Phase Three. 🤷🏿‍♂️
   2b) It was a joy to have its company regardless, though the ending disregarded it completely in my case.