It's mentioned in noted on Falke units that they bear an uncanny resemblance to the two leaders. It's also mentioned that the leader of the Empire was bioresonant and that helped her raise the empire and create Replika,and the Eusan's leaders could well have the same gift that their Replika could inherit. FLKR units are also given more respect and authority than any other Replika and are also crafted as the nation's superweapons, and presumably whoever they were copied from have the mentality to be good leaders. All this plus a bit of ego-stroking make this a likely origin for the FLKR mental pattern.
This is a guess based on the medical records Elster can find. There it is visible that all of the Replika models Elster encounters are dead-ringers to those present in those records. It is certainly a bit odd for every Replika present somehow looking exactly like people Ariane knew at Rotfront. Perhaps those seen are just the result of her Bioresonance mixed with her memories taking the place of the real ones, that is if these Replika models exist at all.
With this guess, Elster died in the initial crash or was already dead before that. However, the location they crashed in allowed Ariane's bioresonance to give her a kind of second chance to fulfill her promise. All the locations Elster visit are not what actually exists on the planet but are rather reconstructions from Ariane's memories mixed with Elster's own creating this weird amalgamations of impossible locations. However, part of Elster's soul was afraid and didn't want to kill Ariane leading to the opposition she constantly faced, with Adler perhaps being a personification of these feelings.
One thing that comes up in several attempts at the game's storyline analysis is how is how exactly S-23 is connected to Ariane's life and memories. The catch is, how does she know all the minute details of the station if she supposedly never had been there and it only shows as an alternate place of employment?
The possible explanations can be thus:
- Ariane imagined the whole mine by extrapolating her knowledge of the world and society. The result most probably scared her a lot.
- Ariane imagined the whole Penrose program participation instead, as a coping mechanism while actually toiling at S-23.
- The time loop is more extended than shown and may feature merging of several timelines. That is, the one where Ariane flies away on Penrose and the one where she fails and goes to S-23 instead.
- One other possible explanation is that the mine segment is not connected to Ariane at all, but instead is actually based on the memories of the original Elster units. It is revealed that the original neural pattern for the Elster units have been lost, and all new ones are instead based on the original Elster unit instead of whatever Gestalt the neural pattern originally came from. The whole segment is something similar to what happened to Falke, where the old memories of Elsters base get mixed with her current ones leading to it being impossible to tell where one ends and the other begins. After the fake ending, Elster manages to gain clarity and remember who she was actually there for.
- One takeaway from this is the owner of original neural pattern for Elster may be one of Alina's squadmates, which also means this pre-Elster was in love with Alina and maybe also had to look for her all the way back.
- One of the first and last things shown in the game is the crash site of the Penrose 512. Elster first goes away from it searching for Ariane, only to repeatedly return to it because of the time loops. It's a bit much for just dream imagery like the island and beach. Considering the Penrose' mission to find other planets, it may well be that they succeeded (eventually, after Elster died and Ariane in cryosleep) in finding Leng. Depending on the timeline, the Penrose might have either crashed in Leng long ago and gotten buried in the mine, or done so recently. With Ariane still in cryosleep, it's possible her Bioresonance grew stronger as she dreamed and slowly died to cancer in the cryopod (in a disturbingly similar manner to Cthulhu in Rlyeh), only to infect the mind of the FLKR unit when she investigated (either physically or via bioresonance).
From what scattered hints we find, Lilith was a skilled soldier and a veteran from some rather brutal conflicts. A lot of whats going on could be a result of Lilith's memories getting mixed with out current Elster. For example, it could explain why Elster thought she was looking for Alina Seo in the beginning. Alina could be someone who Lilith knew
- Documents added in the 1st anniversary update explain that this isn't the case currently, but it is a major goal of bioresonance research — a means to ensure the obedience of replika without needing to rely on psychological manipulation and routine to keep them from "degrading". An Ara unit who discovers the classified document in Sierpinski has a breakdown over it and retreats into a hidden safe space, which the player can visit with the update.
- Adding to this, several characters (Adler, Alina Seo, the Ara in the Dorms) have Ripple-Effect-Proof Memory of an LSTR-S2301, requisitioned to conduct some survey work in the mines around the time the Gate was discovered. It might be that the player is actually controlling S2301, influenced by the Gate to regain LSTR-512's memories, possibly at the same time Commander Falke was imprinted with them.
