Showing off my level 100 team beating the final boss of the game and getting one of the good endings (roughly equivalent to what would be a neutral ending in a Megami Tensei game). This team is in NG++ which increases the level cap (and therefore the difficulty due to enemy scaling) to 100.
In the final mission, there's two events that take place prior to the final boss. The first happens if you let the Housekeeper live in the early mission where you met them. They show up again buzzing around outside a locked door demanding you let them inside. They'll pop into the body of an attack drone, and then randomly decide to join your party or attack you. If you have The Prototype on your team for this mission, I think it's guaranteed to join your team, giving you an extra NPC for the final boss. There's also a treasure chest with a high chance at a super rare top-rank piece of equipment. Because you can't upgrade equipment in the middle of the mission it won't be useful until the next New Game + cycle begins, but good gear is good gear. If you destroyed the Housekeeper I think you can still open this door, but the encounter with the attack drone always results in a fight (that's not too tough to win).
The next encounter is with Riggo, if you let him live. I've never seen him show up when working for Aurora though. It might be there's a random chance he won't show, even if you were nice to him? It's the first time I had both him and the attack drone join for the final boss at once. If Riggo shows up here, he can open the locked Aurora door for another chest with a high chance at top-tier loot (or you can bring a keycard you can get from gaining favor with Aurora, or try to bust it open the hard way with a Hacker, where you get three shots to hack it open before it locks permanently).
The final boss, the Overlord, is extremely dangerous. It begins by giving you a chance to apply buffs, and then summons enemy spawners. They spawn enemies on their second turn, but are susceptible to stuns, so it's a race to keep them occupied while nuking them down aggressively. Don't bother attacking the Overlord directly. It's immune to damage, and its health is tied to how much health the Printers it summons have.
Not the greatest fight, my Void Psyker exploded a few times overloading on void energy and scared off Riggo. :'(
When all four Printers are destroyed, phase 2 begins with the Overlord now becoming vulnerable to attack and summoning four different elemental cannons. Instead of using spread out damage attacks, you're better off using chargeable skills that allow you to burst down the Overlord's stupid eyeball as rapidly as possible before the cannons can mow you down.
Phase 3 is extremely dangerous in a new game file where you're likely still using Heavy Armor. They can grab characters and crush them, denying them turns while dealing heavy damage. However, my team is kitted for maximum dodge %, and basically dances around their attacks. I don't think I get grabbed once. The health scaling at level 100 is so insane that they don't actually display their health as a whole number, but rather show it as an exponent! The claws have over 11 million health and the Overlord itself has less than a tenth of that (about half the health it had in phase 2), so the trick is just to blast the Overlord down as quickly as possible again, though stunning the arms is very helpful to keep them from grabbing you. I actually decided to mess around in this phase since I was doing well, and tried to see how much health I could rip off one of the arms before my various passive effects killed the Overlord anyways. As it turns out, I got at least 5 million points of damage on one of the claws, so that's something!
The ending can go a few ways. You can trigger a bad ending by trying to immediately attack Patil repeatedly until he summons drones to overwhelm you. The Overlord just floats up, unharmed, and after a fight against 5 normal robotic enemies, the game ends with a sequence where your characters are last seen fighting what looks like a hopeless battle.
Tossing the Overlord to whoever comes to the rescue gets you the good ending. If you dawdle too long, you'll get into the hopeless fight as above, and if you toss the drone to Patil, he promptly kills off your allies (or triggers his ending if you were aligned with him).
In the good endings, you have the option to actually kill Patil after whoever comes to your aid has deactivated the Overlord. This only changes the dialogue slightly, but after everything he's put you through, it's very satisfying to cut him down.