This blog post is dedicated to discussion and predictions about what will happen in Part 3 of Monster Girl Quest: Paradox.
We now know that the Lilith Sisters and the three Seraphs come from parallel worlds in which the monster and angels won the Great Monster Wars, respectively. They both have solutions to the problem of Chaos: the monster solution is to kill everyone and use the reincarnation system to merge their souls into their selves in the Monster World; the angel solution is to bring only the few chosen ones to the Angel World and abandon the rest. The endings of Part 2 diverge massively depending on which of Alice or Ilias was picked at the start. On the Alice route, everybody knows about Sonya's and Nuruko's true natures (except for them) and Marcellus has killed Alice XV, which is likely to drive a wedge between Alice XVI and Luka. On the Ilias route, the characters don't know these things but the player still knows, and the Sonya in the party isn't the original Sonya but a copy of another universe's Sonya.
Early Part 3:
On the Alice route, there'll be the additional complication of Alice's mother being killed by Luka's father. This will only be resolved if her affection is above a certain threshold and/or the player has made certain decisions (always talking to Alice during campfire scenes, for example). If these conditions aren't met, Alice will decide that she can't be in the same party as Luka any more and leave. Narrative-wise, this serves as a major difference with the Ilias route.
The destruction and restoration of the Paradox world at the end of Part 2 is unlikely to be without consequences. It is likely to result in an acceleration in chaosization, which will result in Apoptosis leaving the Tartarus and invading the world, as occurred in the world beyond the third Tartarus. This will force the party to choose a side: monsters or angels? This is the true point of no return. I believe that the player will be able to choose either side, regardless of whether they are on the Alice or Ilias routes. This is because it's unlikely that the entire plot of such a long game is going to be dictated by a decision made at the very beginning. However, if you choose the opposite of your route (angels for Alice route and monsters for Ilias route), you will need to have the corresponding character's affection above a certain threshold or they'll leave the party (if Alice has already left, this is no longer relevant). If this happens, the one you didn't choose at the beginning will join you party in their place.
Once the decision is made, you will travel through the corresponding Tartarus (Hellgondo one for Monster World, Esta one for Angel world). Once you do this, you will no longer be able to return to the Paradox world. This will be made clear before you leave, so that you can finish any unresolved business.
Monster/Freedom route and Angel/Order route:
I've lumped these two together as I think they'll proceed similarly at first. In both routes, you'll get access to a complete new world map. There will be still be random encounters so that you can fight all enemies (if not necessarily in the same locations). You can keep your existing party members, explained as the monster/angel factions deciding to give Luka free rein in this (in-universe explanation), and because it would be unfair to the player to lose a significant fraction of the party they've worked so hard to obtain (meta explanation).
You will be presented with three goals: gaining the loyalty of your chosen faction, defeating the opposing faction, and solving the problem of Chaos. For the first one, you'll use the usual MGQ method of defeat means friendship: challenging and beating the Six Ancestors/Seven Archangels in order to recruit them. The goddess of the faction won't be fought or recruited, as they would be too powerful at this point in the game. For the second, you'll go to the opposing faction's world and beat their leaders, including Alice I/Goddess Ilias.
The third is more complicated and hence harder to predict. Judging from Luka's alternate forms in the Labyrinth of Chaos, he's going to somehow become the Worldbreaker in the Monster route and the Child of Judgement in the Angel route. Narratively, these roles presumably involve Luka killing the populations of every other world and choosing a few from the other worlds to save, respectively. Gameplay-wise, these will presumably act as alternate forms, similar to Sara's human and succubus forms.
Also from the Labyrinth of Chaos, we have "Devil Killer/Monster Lord Killer" Marcellus and "Angel Killer" Heinrich. From what I understand of the former, he's out to kill all Monster Lords in the multiverse as he thinks it'll help stop Chaos, while the latter presumably has the same motivation as he did in life. These will be encountered as bosses at some point on the Monster and Angel routes, respectively. Having certain party members (Lazarus, Merlin, Lucifina-chan, Alicetroemeria, Heinrich, possibly Marcellus if you can recruit another version of him) in the party when you encounter them will result in additional dialogue.
There's also the problem of Kagetsumugi and her army of legendary monsters. It's been debated whether the Black Alice she serves is the same as Goddess of Chaos Black Alice, but either way you'll need to fight them. Afterwards, you'll be able to recruit them (in Kagetsumugi's case, you'll probably need to fulfil certain conditions relating to Chrome and/or La Croix first).
And then there's the role of the original universe in all this. We may get to see the original universe's characters again, though it's unlikely that they'll be recruitable as that would result in too many basically-identical copies of characters in the party. Nero and Neris will certainly be recruitable, since by now they won't be overpowered compared to the rest of the party.
Finally, if Alice/Ilias left the party earlier on, they'll show up again as a boss, potentially with a party of their own. This won't be a particularly challenging fight, but it will certainly be a personal one.
After everything else has been solved, you'll be able to strike at the source of Chaos, Black Alice. You'll first be faced with a gauntlet of weaker bosses. The first two will be a fully-powered Adramelech and a version of Sonya, within expectations. The third one will be something unexpected: the goddess of your own faction, Alice I (Monster route) or Ilias (Angel route). They will have been controlled by Black Alice and forced to fight you, since she thinks that this would be fun. Why do I predict this? I think you'll be given the opportunity to fight virtually every enemy, regardless of the route, and this was the best explanation I could think of (as the alternative would be to have Black Alice being outsmarted and taken over again). Finally, you'll fight Black Alice herself.
This is similar to the ending in the original trilogy that you get by killing Alice at the end of Chapter 2. This involves siding with Black Alice. To be honest, I can't really think of an in-universe explanation for Luka making such a decision. The best I could come up with was that Luka decides that the Monster and Angel Worlds are both evil and it would be better for everyone to be consuemd by Chaos.
This route would be kicked off by Black Alice making contact with Luka early to midway through Part 3. If he accepts her offer, he gains access to a new form (Luka Chaos?), not necessarily immediately. He is tasked with defeating both the Monster and Angel Worlds, as well as Reaper and White Rabbit, leaving Black Alice with no opposition. This decision will cause most of the party to leave unless they have maxed out affection and/or other requirements are fulfilled. At the end of it all, Black Alice has turned the entire universe into her playground. She rewards Luka in the manner expected of this series, leading to special H-scenes that are inaccessible on any other route.
An optional prerequisite for this route would be for you to complete at least one of the other routes first. The narrative explanation would be that the Black Alice you defeated sends a message to herself in another one of your game files, warning her and advising her to try bringing Luka to her side. Given that Black Alice is shown to be capable of seeing into other universes and times, this doesn't seem like an impossible feat for her.
This is the route where you manage to achieve the impossible feat of saving everyone, and so is naturally the hardest of them all. As a prerequisite, you would need to finish the game on both the Monster and Angel routes, or both the Alice and Ilias routes (via New Game+). Once you do this, you'll unlock an additional, special NG+ option. This would take you back to the beginning of the game (or possibly just to the start of Part 3), but unlike the normal NG+, Luka (and possibly the rest of his party) canonically retain their memories. This allows them to accomplish things that were impossible in the previous playthrough: defeating both factions using only their own power, making the factions work together, and saving everyone in every universe. Even saving Black Alice might be possible at this point.
These are my thoughts on what could happen. I haven't gone into all the possibilities - there's still one Tartarus unexplored, for example - but I think I've covered most of them. Please comment with your own thoughts on this.