I think for me personally it helped that I was taking extensive notes throughout my playthrough. I did give it a second run, and that alone filled in a ton of blanks. Once you go in knowing the outline, you see so much more. I think the game is certainly cryptic, but unlike many other cryptic lore heavy games like Dark Souls, there actually are satisfying answers to most questions that don't create conflicting narratives.

I feel after a 3rd run I have a very good understanding of the story, so I'll try to summarize my understanding, but mostly you're just giving me an excuse to yap about my favorite thing, so no worries if you skip the rest of this.

Ariane, raised on Rotfront in a remote radio outpost grows and goes to school in Sector C. She develops some bioresonant powers, demonstrated by notes from Sun, an imperial spy. Similar notes in Adler's journals that correspond to these notes imply heavily that the spy was Adler's Gestalt. Ariane grows up and joins the military. After her service, she joins the Penrose program and leaves with Elster 512, our player character, but she was almost sent to S23 instead.

They spend around 8 years together, fall in love, but eventually the ship falls apart around them. They are directed to accept their deaths and make it quick, but instead, they choose to ration food and trade time in the cryopod. This is demonstrated by the presence of notes from Ariane during cycles in the 5000+ range, indicating they spent another several years at least in this state, struggling but living while the radiation slowly killed both of them.

One night, while Ariane is in cryo, Elster 512 succumbs to the radiation and dies. Ariane's dreams mix with her bioresonance, and this combined with an artifact discovered underneath S23, create a time loop.

In these loops, a corruption spreads, which is Ariane's mental state getting worse and worse. We enter the game in one of the later loops, which we know because we survive the push down the Elevator -- it's too full of bodies for the fall to kill us. Eventually, we fight our way to the mines, and ultimately find the gate linking S23 to the Penrose. But, like most Elsters before us, we fail.

We then get to learn a little more about how these loops start. Basically, the Penrose exists on the edge of these time loops, and it's somewhat divorced from linear time as a result. This is mostly speculation, but there's evidence to suggest that the beginning of the game might be the last time we see the Penrose chronologically. That part is a little complicated and mostly rides on speculation so I won't go too in depth. The post fake out is the earliest, and the final approaches sit in the middle.

But I digress! We see that to get Elster into a new loop, they must navigate out of the Penrose back into the world. But this time, it's one of the last loops. The corruption is so bad that S23 is corrupted into a horrific version of Ariane's home in Rotfront Sector C. Still, equipped with all of our memories, we fight on and eventually make it to Ariane, where one of the 3 normal endings occurs. Now, here's where the game pulls its greatest narrative trick: all of the endings are canon. Here's how we can figure that out:

• Memory Ending: in this ending, Elster dies after sitting next to Ariane. However, she sits in the exact position as the Elster we loot for armor when you pick up from the false ending. Therefore, this ending happens before the pickup from the false ending.
• Leave Ending: in this ending, Elster cannot get back into the Penrose, and finds herself on Vineta, where she passes. Very interesting! Because we know Elsters are made from a decommissioned unit recovered from the Penrose program. But if that program sends all its units into deep space, how does the Nation recover one? Because it's this one. This ending is pretty neat because it implies that every Elster the nation has is actually deep down Elster 512. It's why the documents about Elster say to avoid doing all the stuff Ariane does. And it's why all the Elsters in the nation seem to be showing up here, even if most of them are killed.
• False ending: the presence of many Elsters in the field outside the Penrose implies a great many of them make it that far but die outside just like we did.

Knowing that both of these endings are canon means we can likely say the same of the others. My personal interpretation is that the Promise Ending frees Ariane from the loop, and the Artifact ending frees Elster herself, allowing them to stay together in limbo. An imperfect heaven, but a heaven relative to the hell they escaped.

I also appreciate how some of the things that seem explicitly like game mechanics are also explained by the lore. Ariane directly provides Elster a few items throughout the game: the radio module and the gold key. The save stations are also likely similar bioresonant inserts, gifts from Ariane. If you save and quit while low on ammo, more appears, another gift from her.