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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
War Frame
The series takes place post-Mass Effect, after the Destroy ending.

(Ending spoilers for Mass Effect 3, obviously)

  • In the aftermath of Shepard's sacrifice and a great deal of technology being lost, along with the Mass Relays, and with the Reaper war leaving planets in ruin and no longer distracting the many organics from in-fighting, it's not long until another war springs up. Earth is still reeling from being the hardest hit of the Reaper war, and with much of the Alliance in tatters, rebel groups begin picking up steam in the resulting chaos. The remnants of Cerberus that managed to stay in the Solar System, still indoctrinated to the Reaper cause, begin to band together and link up, holding on to the data that they gained from Sanctuary. With the Alliance's hands tied, they're able to convert desperate civilians and rebel groups to their cause by indoctrination. Over time, Cerberus' weapons and armor improve, while they refine their research, making breakthroughs in cloning, flooding Alliance military with dumb human clones that are just as strong, durable, and hulking as the krogan - if not faster. Soon, the bulk of Cerberus are easy-to-control clones, and they manage to take over a ruined Earth.
    • Somewhere else, the shattered remains of the extra-judicial corporations that avoided the Citadel as much as they could decide to salvage what little there is they can find of the Reapers, and begin attempting to make AI from scratch once more. They plan on taking Earth for their own means, as well, ruling it as a corporate utopia. Using "orokin" - really Reaper tech - to Indoctrinate survivors to manufacture Reaper-based tech and AI-controlled robots, as well as managing to reverse-engineer Mass Effect relays to fashion a transport array through the system, called the Solar Rail, they begin to attack Cerberus's forces and dominate whatever other colonies that survived the Reaper war.
    • As for the Reapers themselves, they unleashed a last-ditch attempt to "preserve" organic life, in their own twisted way. What's known as the "Technocyte plague" is spread from the use of Reaper artifacts, a more potent and faster alternative to Husks, to destroy any organic who comes in touch with them.
    • And what's left of the Alliance forces and stranded aliens in the solar system are slowly being re-awakened by a secret resistance force, only known as the 'Lotus'...

zero is a Warframe.
Do i even need to explain this one? Zero not only look similar, his illusion power is similar to some of the 'lower key' things a Warframe can pull off and he comes stock standard with a sword just like all the other Warframes (save the ones that go for hammers, but I digress).
  • Jumping off of this, the Corpus are either the distant past or distant future of Hyperion. Both factions use robot weapons platforms in conjunction with squishier cybernetically-enhanced humans and flying support units that can create shields.

All Warframes are just advanced Nanosuits.

All the enemy factions are shout outs and take that to other games
each enemy that you take out by the dozen is based on a popular game series.

Grineer : Krogan from Mass Effect and Starcraft Marines.

Infested: Left 4 dead and Deadspace. Possibly even the Flood from Halo.

Corpus: Maybe the Protoss from Starcraft.

  • ...It would probably be more accurate to say that the enemy factions are based on the enemy factions initially present in Mass Effect 3's multiplayer, which features very similar baseline gameplay:
    • Grineer=Cerberus; both are armies of human soldiers with cybernetic augmentation, and they both feature "riot shield with pistol" units.
    • Corpus=Geth; both are armies of robots that use small, flying drones, generous amounts of shielding and often back up their rapid energy attacks with stagger/knockdown attacks.
    • Infestation=Reaper; both are armies of zombified members of other factions in the universe, swarm the players in large numbers, feature little in the way of armor or shields for the rank-and-file but heavy armor for the more powerful "leader" units, an overarching vulnerability to fire and unusual status effects that can quickly kill an unprepared player.

All the leader speak Simlish due to them being the most genetically degrated.
At least for the Grineer, the Corpus all speak Simlish.

The series takes place in the PAST, not the future.

The Tenno deal devastating blow after devastating blow to both the Corpus and the Grineer. Eventually, the Grineer either are wiped out by the Tenno or degenerate to the point that they all perish. The Tenno use Orokin technology to terraform Earth and make it habitable again, deciding to restart their society on it and hanging up their Warframe suits in hidden locations across the world. The Corpus, seeking a less hostile market, leave to other parts of space, or are killed off by the Tenno. Certain Corpus members who overcome their brainwashing remain on Earth to colonize it, although on different parts of the world from the Tenno. Gradually, the humans forget about the Warframes and neglect Technology because it's arguably the reason behind many of the game's problems. Over time, each separate group of humans develops into its own civilization, and things go from there.
  • Possibly a joke, but the developers have stated on a live stream that Hayden of darkSector was the first of the Tenno, which would put a crack in this theory if Dark Sector took place in present day.

The Lotus is an AI.
In mobile defense missions she says "Plug me in". Not plug my 'hi tech hacking whatchamacallit' into the network. plug me in.
  • Could be a man-machine interface like in The Matrix, Shadowrun etc.
    • This is very much likely, as her new-ish animated image appears as a woman attached to numerous thick wires.

The Lotus was one of the Grineer Ruling Sisters.
She never really goes into her reasons for anything but certainly has a big problem with the Grineer. We know the Grineer are power-seekers who want to control everything, and Captain Vor refers repeatedly to the Ruling Sisters who are, presumably, in charge. The Corpus also refer to Lotus as 'traitorous' in one of their transmissions. And while most of the assassination targets make sense, a few of them, namely Vay Hek and Tyl Regor, stand out as being people with little to no military importance. Vay Hek is just a politician and Tyl Regor is a researcher trying to cure the Grineer genetic deterioration, which seems important until you realize the deterioration doesn't stop them from cloning soldiers anyway. But they do make sense if Lotus were a rogue Grineer - The best way for her to get power without needing the other ruling Sisters would be to hijack command of her own force - the Tenno - and use them to get rid of the competition for Orokin artifacts, namely the other Grineer and Corpus. Vay Hek is a senior politician, and likely an old one, and he may very well know too much for Lotus to be comfortable leaving him around while killing Tyl Regor ensures the Grineer can't be cured of their deterioration, resulting in an eventual bloodless genocide with her the only Grineer left standing. So why would Lotus survive when all the other Grineer are dead, and why would she want to use a plan that could take thousands of years to work? Because, like General Sargas Ruk, she went the cybernetic upgrade route, but with the greater resources of a Ruling Sister (and possibly some help from Corpus) she was able to succeed and become completely technological, rendering her immortal as well. She wants the General dead as well to make sure he doesn't succeed, that way she can be sure to have no competition.

This means her stated reasons for wanting some of the assassination targets dead aren't her real ones. They are, instead:
  • Councilor Vay Hek knows too much and has to die before he connects all the dots about who Lotus is.
  • General Sargas Ruk is potential competition if he ever 'ascends' to a purely machine state like she did.
  • Tyl Regor needs to die to make sure the rest of the Grineer eventually die, too.
  • Sgt. Nef Anyo originally sold Lotus her first Tenno soldiers. Killing him means she can seize the rest of them for free.
  • The former boss of Pluto wore a hat that looked very similar to the Lotus' own.

    • Disturbingly, she refers to a Tenno hibernation pod in the defense missions as "equipment."
    • This may be untrue, as Grineer lore states that the sisters consist only of twin Queens. Unless they struck her from the record for her betrayal...
    • The Corpus refer to all Tenno as "traitorous" because they worship the Orokin and their technology. The Tenno are responsible for wiping them out.

There is more than one Lotus. You've been talking to more than one.
In one mission successful message, she mentions the "Lotus will be pleased with us." Also, at least for the Grandmaster rank, clicking on Rank gets a reverb that sounds like multiple Lotus talking to you.
  • In missions where she suddenly "changes her mind" and tells you to kill everyone on a ship; that's the group overriding the initial Lotus's orders.
  • Possibly Dummied Out or Retconned, recent updates have changed her message to "I am pleased".
  • There's a fan theory somewhere that explains the Retcon as Lotus becoming more accustomed to a Hive Mind

The Orokin had interactions with the Forerunners.
Look at the orange glow of the dematerialising Capture targets and tell me that isn't a Composer in action.
  • Warframes are just an evolved Combat Skin.
  • And the Tenno being Composed uploads would explain their being able to Body Surf between Warframes with ease.

The Warframes are alive.
Tenno seem to be hermaphroditic or possibly even unisex organisms/energy beings due to their ability to equip any Warframe and gain or lose various sexual characteristics. However, when the Lotus refers to the Warframes she uses phrases such as "he is a force to be reckoned with" or "use her wisely"- the Tenno don't have genders, but the Warframes do. It's possible that the Warframes aren't just high-tech suits, but some kind of symbiotic, artificial organism initially engineered by the Orokin.

The playable Tenno are the last remaining descendants of the Orokin.
In a very Assassin's Creed-esque way, the Tenno are capable of using Orokin technology (artifacts, Cells, Catalysts, Reactors, Primed weaponry) to its higher capacities due to their Orokin blood. If Lotus isn't a Tenno herself, this would give an interesting twist as to her reasons for using the Tenno.

Going off of this, Stalker is not only not a Tenno, he isn't even a descendant of the Orokin, but of their enemies the Sentients. This would explain how he is able to find and kill the Tenno so easily: Sentient technology designed to track down, counter and destroy Orokin tech. Doesn't it seem coincidental that he is not only equipped to kill Tenno, but that he came into prominence soon after they awakened? Unless the Lotus woke him up around the same time to use him to collect Orokin technology...
  • The Stalker half is Jossed by his Codex entry.

You are awakened by a mysterious party and sent to complete missions that usually involve killing lots of people in gory, violent ways for little more reason than your quest-giver's say-so. The more you learn, the more you gain a nagging suspicion that maybe you're the real villain of the piece...

The real identity of the Stalker is Zer0 from Borderlands 2.
After coming into contact with the Eridians, he gains supernatural powers, granting him the ability to teleport (and leave behind a puff of smoke). And so, he ventures into the Sol System in search of new challenges, and of course, sees the Tenno as a worthy foe. The in-game reason behind him attacking Tenno is stated as avenging a particular boss, who, more or less, is an apathetic person/entity, but then again so is Zer0. Also, his frame is also black, just like his default color scheme(albeit his head is more sinister looking). And last but not least, one of his class mods in Borderlands 2 is called "Stalker".

Alad V will be a future Assassination Target.
Alad V, the Corpus executive responsible for Operation Arid Fear, is the only person on any side in Warframe to have ever noticeably caused the ever-calm Lotus to lose her cool. All throughout Operation Arid Fear her voice betrays the fact she's seething mad behind her usual calm demeanor and at times it almost sounds like she's pursuing the Corpus scouts specifically to spite Alad's planning. The whole 'eyeless slag' comment certainly didn't help things, either. Lotus is going to order the Tenno to assassinate him eventually whether it's useful to her objectives or not simply because she hates him that much.
  • According to the developers, Alad V will end up being the closest person to knowing the true nature of the Warframes... other than the Lotus herself.
  • Alad V is certainly significant as he was also the mastermind behind the previous Operation Sling-Stone.

Confirmed as of Update 11.

Tenno Eventually Stop Listening To Lotus And Join Different Factions.

From running tasks with no specific information or explanation as to why Lotus wants you to maul a ship full of Corpus workers or steal a few data masses to accepting certain suicide missions where no one will leave alive (survival missions where you only "win" by letting your oxygen supply run out) the Tenno begin to question why they're even working for Lotus as well as her motivation for wanting to wipe the Grineer off the map. Receiving no reply and not wanting to end up like the groups of Tenno covering for "Alpha Team" by dying of asphyxiation, they break off from the Lotus's command and seek other work, to which Lotus responds by sending Tenno still loyal to her to assassinate these "traitors".

The few Tenno that have abandoned Lotus decide they've no choice other than to join the Grineer. The Corpus'd want to rip their Warframes to pieces and take whatever they can salvage, they're not crawling back to Lotus, they can't join other Tenno as they don't know which ones to trust, and standing alone would get them killed by the Lotus-loyal Tenno. Although skeptical at first to see a Tenno want to join them, the Grineer realize these guys are for real and start accepting more and more of them into their force. They deck them out in Grineer heavy armor, give them some weaponry, and pit them against the Corpus and other Tenno that're hungry for some Grineer blood.

Seeing the teal, large-shouldered Tenno under Grineer command rip through their workers like wet tissues, the Corpus decide, "Alright, we've got these Tenno corpses here, instead of butchering them for parts of their Warframes and selling them on the black market, why don't we cut in some of our technology, make some Tenno-cyborgs, and make them fight for us?" Accomplishing exactly that, the Corpus now have their own variant of Tenno to combat the Grineer as well as hold off the Lotus.

Meanwhile, while the Infested are chewing on Corpus, Grineer, and now Sentinels, they also decide to posses some of the Lotus's former forces and turn them into their own. Now you've got an Infested Rhino tanking loads of damage shambling alongside an Ancient Healer and an Infested Volt sending armies of Chargers dashing towards you at ludicrous speed.

So, now you've got the tanks of thick armor and Orokin technology, commandeered by the Grineer, pit against squishier, but equally-lethal, robot-Tenno working for Corpus also fighting off the infected zombie space ninjas controlled by the Infested who are also trying to take down the Lotus's Tenno, still adamant to wipe out the Grineer and Corpus forces and their new Tenno allies.

The Stalker is just a guy with a twisted sense of balance and order

He only attacks those who have killed bosses. Then, once he executes his target, he leaves.

Why is he so crazy? Maybe he dated Nyx once.

Jossed with the new Codex entry, which shows that he hates the Tenno because they betrayed the Orokin.

The "new" Lotus is the true Lotus, and the one who's been with the Tenno through Closed Beta and Open Beta is a separate woman slowly assimilating into the real Lotus' consciousness.
Just like the Tenno, the Lotus has lain dormant, asleep for centuries. In order to awaken the Tenno and fight back against the Grineer and Corpus that have destroyed all she had, a woman who lead the resistance manages to break into an Orokin tower and assumes the mantle of the Lotus to get rid of the two factions once and for all. At first, it was simple - wear the hat, act like a noblewoman, pretend to be a mighty tactician, making some mistakes here and there like saying 'The Lotus will be pleased" instead of 'I am pleased'.

The Neural Sentry for the Tower, however, is different.

The woman eventually finds her voice changing, memories she didn't have yesterday flooding her mind. She feels herself becoming the mask. This would explain why she weaves in and out of a modulated voice, along with her newer voice clips.

The Orokin were the bad guys, and so is Lotus.
The Orokin and Sentients were different cultural/ideological factions of the same species- in the same way humans divide themselves based on nationality. The Orokin were a hierarchic culture that focused more on pragmatic, manipulative, even fascist methods while the Sentients had a deeper sense of honor, justice and equality. These conflicting ideologies escalated to all-out war, with the Sentients likely trying to correct some wrong the Orokin caused for the sake of progress (such as creating/deploying the Neural Sentry against an unsuspecting lower class to keep them in line). The Orokin, true to their pragmatism, unleashed the long-contained Technocyte Virus upon their enemies, and when that failed, turned to the Tenno, a small faction of deadly but untested warriors. The Tenno fought the Sentients, but even as they wiped out their enemies they came to understand their reasons and adopt their philosophies (and seeing a few of them mutate into Ancients couldn't hurt either- Golem did say, after all, "We are your flesh"); in the end, the Tenno turned and slaughtered the Orokin as well. The Stalker was a lone Inspector Javert among the Tenno, possibly even The Dragon to the Orokin leader (thereby sticking to his beliefs that the Orokin were incorruptible and the traitorous Tenno were to be punished); he might have even been the first Excalibur, if not a prototype. The Lotus was an Orokin survivor, possibly even the one who originally locked the Tenno away, and has now awakened them to prepare the galaxy for the return of the Orokin Empire (purging the Tennos' cryopods such that their memories would be lost was calculated). The Lotus leaks information on Tenno whereabouts to the Stalker to dispose of them when they get too close to finding out the truth (as they might after the various exposition-filled boss battles)- or if they simply survived a suicide mission- and he complies to his lone master.
  • Because let's face it- the Lotus is accented with gold. Gold only represents one thing in Warframe; she just toned down on the white.
  • Bonus points if the Sentients end up being based on samurai.

The Orokin were human, so were the Sentients, and the Tenno were mind-controlled.
Alright, so, recap of what we know: mysterious race Orokin fight mysterious race Sentients, Orokin find that the Void mutates members of their race, and use those mutations plus super-tech to make kick-ass soldiers. With me so far? Cool. Since the Tenno prtty much look human, and since we know they used to be Orokin, we can then infer that the Orokin were also human. Now, on to the theory.

The Orokin and the Sentients were both human. The conflict between them wasn't an alien invasion or an attempt to conquer, it was a civil war. The Orokin embarked on the standard campaign of dehumanizing your enemy that seems to happen in most wars, and were either wildly successful or the war went on for so long (or both) that people actually stopped thinking they were the same race. So, they fight. The Orokin start to lose. Then, they find out that this Void thing mutates people and gives them people superpowers. Then, they find a way to turn these mutants into Super Soldiers. Awesome! But what's even better than Super Soldiers? Mind Controlled Super Soldiers! You wouldn't want your soldiers who were deliberately exposed to potentially torturous and traumatizing events that gave them superpowers to walk around without control bolts, would you?

So, the Tenno, wearing those nifty control crowns you can see on the Corrupted, start to fight the Sentients. Maybe they even go along with the control crown thing, were told they prevented the Tenno from going crazy because of their experiences. But then, in the process of their fights, the Tenno discover that their adversaries aren't aliens at all, they're really other humans fighting for... something. Survival, maybe. And suddenly, a heroic campaign to protect the human race from extinction turns into good ol' genocide. The Tenno (or most of them, at least; see below) want to stop. But those fancy crowns won't let them; the Orokin programmed them to keep killing Sentients until there's nothing left.

Eventually, the war is over, and the Tenno come home hailed a saviors by the public. But, there's a problem: the Tenno are no longer under Orokin control. Maybe they found a way to subvert the crowns; maybe the Orokin forgot to program in a "don't turn on your creators" subroutine; maybe all commands were only programmed in light of the war, and with the war over the Tenno became free again. Not sure. But in any case, the Tenno come back, pretend to still be loyal soldiers, and, once they get close enough, skewer their former masters. The Tenno go on a rampage, killing both the Orokin scientists who brainwashed them and the leaders who ordered it to happen. Eventually, everyone who knows how to make or work the advanced technology is dead, and the Orokin survivors are scattered, beginning a dark age that leads to the rise of the Grineer Empire and Corpus company, while the technocyte plague the Orokin developed for war runs out of control.

So the Tenno got their vengeance. But they still have those crowns, and they don't want someone else coming along and figuring out a way to program them again. So they try to remove them; problem is, they killed everyone who would know how, and their own attempts have... unpleasant consequences. Namely, massive brain damage. Eventually, through trial and error, the Tenno find a way to remove the crowns and stick themselves into healing/stasis pods that slowly repair their damaged brains. Problem is, complete amnesia is still a side effect, and the healing takes time. Lots of time. So, the Tenno make preparations to initiate healing en masse and leave someone behind to watch out for them. Like the Lotus. Or someone who the current Lotus killed before taking her place. Or something. So, time goes by, the Lotus is replaced or controlled or decides it would be awesome to use her former comrades for personal game, and so upon awakening the amnesiac Tenno lies to them and uses them for her own gain.

But what of the Tenno that didn't disagree? The ones who thought the Orokin were right, brainwashing be damned? Well, they stay active while the rest of the Tenno go to sleep and forget themselves, watching the system, or even the galaxy, descend into chaos and develop a bitter hatred for their traitorous comrades. They call themselves the Stalkers (yes, they, I refuse to believe it's just one guy) and wait for the Tenno to wake back up. Because they don't want the Tenno to die peacefully in cryosleep, oh no. They have to suffer. So they watch, and wait, and try to protect the remnants of Orokin civilization that humanity has become.

I might come back and clean this up later, I realize it's kind of a mess as is.

It's not "Orokin", it's "Awoken".

Hayden Tenno is the Stalker
Hayden Tenno is confirmed to be the first Tenno. Seeing as he was likely rescued by the Orokin at some point and possibly their first in command, it would make sense that he would be loyal to them. Similarly, the Stalker's frame resembles the Excalibur, confirmed to be the first warframe. He could be something of a Super Prototype, which is why his powers would later be used and adapted to other frames.

The Grineer and Corpus factions will suffer from infighting and split into to smaller groups.
We've already seen that Corpus don't necessarily work out all of their inner conflicts peacefully during the Alad V event where Frohd Beck was willing to sell Alad V's location out. Players will notice that the crewmen in Jupiter, where Alad V is located, have differing main weapons and proxies at their disposal compared to the main bulk of the Corpus, showing the split within the faction.

Sargus Ruk and Vay Hek also seem to be at odds with each other as a result of Hek's releasing of the Grustag Three. Sargus Ruk explicitly calls Hek out on this move and basically condemns Hek to whatever fate befalls him.

It seems more likely that with the upcoming Proxy Wars system as told by DE, that Tenno can choose these splitting branches of the Corpus and Grineer as one of the factions that they will support.

The Stalker was originally a zero-tech

He built his suit out of Tenno he sniped. He may also have later shared the Dispel tech with the Corpus, or the other way around.

The Sentients were Hiigarans or X-COM.
The lore says the Orokin were forced to resort to the Tenno because the Sentients just reverse-engineered everything else that was thrown at them. Who else would fit better than these gods of ganking enemy tech and turning it on the original users?
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