I proceeded through Warframe at a positively glacial pace, and didn't do The Second Dream until I was past MR 14. I liked to spend a lot of time unlocking every node on every planet, trying out new weapons and warframes, and did not place a high priority on the quests. This left a lot of time for idly dreaming up fan theories to connect various bits of lore, as follows. Hopefully it's interesting to at least some of you.
The origin system's history was divided into two parts. Orokin were the ruling human class (subspecies) in the solar system. When they were defeated, those who used to be their subjects formed the Corpus, Grineer, and various smaller communities such as Cetus and the one we meet in The Glast Gambit. The current "tutorial" introduces the Grineer and Captain Vor, who wants your starter warframe for its ancient human DNA, with which to revitalize the mutation-ridden Grineer. I am not sure why they can't take DNA from literally anyone else, as there seemed to be plenty of human NPCs and enemy Corpus. This tutorial does imply that warframes were humans the Orokin made into "living machines" for the purpose of combat in an old war.
Infested enemies definitely seemed to be some sort of escaped bioweapon or biotechnology tool. Perhaps the Sentients brought it with them, or the Orokin used it to fight the Sentients. Warframes might have been made to fight the infested.
From the Natah quest, I thought that Sentients were Orokin who had, unimaginable millennia ago, traveled into deep space and taken up residence in other solar systems. The journey and eons of separation changed them into unrecognizable forms, and faster than light space travel rendered them sterile, but they wanted to conquer the origin solar system from the Orokin they no longer felt kinship with. I got this idea because Hunhow looks like a crispy version of the Lotus, I thought the Lotus was Orokin, and the Lotus looked mostly human. I suspected the Lotus was either a digitized or simulated personality of someone who used to be alive, since it felt like the Orokin fell such a long time ago, and for all intents and purposes the Lotus was just a disembodied head that told you things every now and then. Or perhaps she was part of the machine her helmet connected to. I was very surprised to see her there in person in The Second Dream, I expected her reveal to be us traveling to where she was, and finding that her human body was inseparable from the machine she's connected to. Perhaps radical life extension is what turned the Orokin who left the origin system into Sentients. A lot of Orokin tile sets have white glowing tree root or branches, and the Eidolon teralyst is made of the same material. The sentient enemies we encounter in-game seemed like they could be for non-human utility, similar to how Corpus use moas and ospreys, so not actual Orokin themselves.
From The Sands of Inaros, we learn that the Orokin took children from villages. Despite the best efforts of the Warframe community, I was aware that operators existed, but I didn't know anything about them. I thought that the Orokin needed children to pilot warframes, but either didn't want to sacrifice their own or couldn't produce their own, so they harvested the lower, non-Orokin classes. Something about the potential and adaptability of children being why adults couldn't pilot warframes.
I thought the Lotus, having switched sides as the Natah quest says, saved a bunch of warframe pilot children by putting them on orbiters in a dormant state until they could be connected to a new, unused warframe unearthed from the ruins of the old world. Then we'd be "woken up," and the game begins. Our true nature hidden from us so that we view the Lotus as a mother figure, and will willingly do missions for her rather than trying to find our biological families who are probably all thousands of years dead.
I also thought that the operator's physical location in the orbiter was in the mysterious technology node near the back where the three doors are. I probably saw
a screenshot similar to this, but without showing the entire field of view, so it looked like the human figure was sitting up from inside the ship. I'd heard the name "the man in the wall," but didn't know what it meant. I thought perhaps it was some kind of energy being or AI that could talk to you through technology, as in a literal voice that comes out of a random wall you are passing by. Or perhaps it's a person integrated into a machine similar to the Lotus, but who was built into a wall as some sort of eternal punishment or means of hiding himself.
When you first visit Cetus, you see the Orokin tower off in the distance, and on the beach nearby, some Cetus workers cutting a slab of meat. One friend of mine thought this was some sort of whale or large sea creature, but if you look closely it's a piece of the tower! The gate into the Plains of Eidolon also helps show this, with a sign made of a bone-like bit of the shell from outside of the tower in the tunnel between Cetus and the Plains. The rust-like patches on the gate doors look like the edges of the Orokin tower in the distance, near where chunks are being harvested. After this revelation, it felt pretty weird to be in the Orokin ship tile sets. All of this tells us that biotechnology with a decorative shell was something the Orokin could do, similar to warframes. If they can grow towers, it seemed like no great stretch to think that they applied this same technology to themselves, for life extension, decoration, or utility.
The above were inspired largely by various science fiction books, in addition to half-understood warframe lore.
Man after Man and the similar, but freely available All Tomorrows (warning: contains artistic nudity and some body horror) contributed the idea of one species splitting off into two or more that no longer view each other as friendly, leading to war and destruction.
The Snow Queen series contains fractured remnants of what used to be a unified human empire. The machines and nanotechnology of past ages are still ticking in some places, seeming like magic or monsters to those who don't know better.
Shade's Children is a story about kids being harvested by those in power to be used in combat.
Various books and short stories by Kameron Hurley. Her writing has a lot of biotechnology and body horror.
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