Theory from Discord server:
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While it seems pretty clear there's a cycle being followed - Idriel's whole thing with the coin is about as subtle as a marching band in a library - I sincerely doubt that the events of Eternum are some kind of time loop.
First and foremost, we know that Eternum is not a computer program. That's kind of the whole in-universe twist: this thing everyone
thought was a computer program is actually just the multiverse. It would be kind of dumb to then turn around and go "actually, it
is a computer program, you're just part of it too!"
Now, that doesn't mean time loops are impossible; obviously magic exists in many planes of existence, so it's probably doable if you have enough arcane energy to just keep the multiverse going in a circle. Unlikely, but possible. What I struggle to see in that scenario is a motive; in the Matrix it was to patch out bugs while keeping human consciousnesses active so they could power machines, but what does the Founder(or whoever is causing it, if it's not him, but I'm going to assume he's the big bad for the sake of this post) gain from looping the universe? We just don't know right now.
The only motivations yet attributable to whoever is pulling the strings are the elimination of the xenomorphs, and the collection of the Gems of Doom. I have...
doubts that wiping out the xenos is gonna be the main plot, given they weren't introduced until halfway through and have mostly been mindless killing machines. Also because, if whoever's doing this has an actual altruistic motive, I don't think they'd be so secretive about it.
So that leaves us with the Gems of Doom. I think that's the key. Someone in here suggested they work kind of like Dragon Balls, where after being used they scatter, and I think that's probably about accurate.
Abstergo Ulysses obviously wants people to gather them but the promise of just handing over the company seems... far-fetched to say the least. Whether they outright grant wishes or just immense power to do a thing is hard to say right now. But they're almost certainly the key to whatever grand design is going on right now.
So back to the cycle. I don't think everything that's happened so far has happened before - not exactly, anyway. It seems likely that the Founder has done this before: set up shop in a world, give its denizens access to the multiverse, and trick them into hunting these stones for him. After he gets them, he presumably just offs them and does as he pleases. Whether things are going according to plan or not at this moment in time is hard to say.
We know that he's aware of Orion, that Ulysses keeps information to track people who collect Gems, and that they can measure a person's affinity with Eternum. All of this is to say that, as of right now, we're still playing his game by his rules. He's confident that we're not a problem yet. My guess is that Thanatos was playing outside those rules, and that's why he got got, but whatever happened he's still a thorn in the side of the Founder. Everyone who gathered the Gems in the past fell into the same trap, ultimately beaten by the Founder who then took power for himself to do... whatever it is he's doing. The plot is going to hinge on us doing the thing he doesn't want us to do, but until we know what the Gems are actually for we don't know what that thing is going to be.
As a final aside, I sincerely doubt the plot is going to come down to "save the world or save your girls, but not both." Not only would that be a huge downer ending for a romance game, at least as the default ending, but it just isn't Cari's style. Remember that OIALT told you late in the game that you'd only be able to take one girl with you after everything was over, but the canon ending was still the one where you just said "nah, fuck that." Even if a harsh choice is presented to us, there will absolutely be a way around it. It may require a sacrifice, in the same vein as Asmodeus, but I'm fairly confident we'll save the world and settle down with the girls to live happily ever after. That's just how it goes.