Foreword
This page outlines what is known and what is highly probable/heavily hinted at by multiple sources (in-game, from Dark Sector, from the devs during livestreams) about the history and story of the Warframe/Dark Sector universe.
Disclaimer
While we were able to find solid and legitimate supporting evidence for essentially the whole story as it is written, it comes from a variety of sources and each of those pieces of information were likely written by a number of different people. We took in all of the various bits of information that presumably even Digital Extremes hasn't fully explored and produced a sensible and logical story from it that probably wont be far off from what eventually gets released officially, assuming they don't change any of the existing background information.
This page and the story will be updated as Digital Extremes ('the devs') release more confirmable information.
The Story/History of the Warframe Universe
Dark Sector Era
WARNING: Contains Dark Sector spoilers!
- This section has been intentionally abriged at the request of the Warframe Wiki's administrator. If you would like the full story on Dark Sector, buy and play the game or read its wiki here.
On Earth during the cold war, the United States invented something called the Technocyte virus. It remained unused and largely untested for a number of decades until 'The Agency' sends a submarine with infected aboard it to the Russian island of Lasaria. A supposedly rogue member of The Agency named Robert Mezner, a specialist in 'nanotechnology as it applies to bioenhancement' is sent to Lasaria secretly to test and propagate the virus among its citizens.
Another Agency agent named Hayden Tenno is sent to Lasaria to kill Mezner and is soon attacked by Nemesis, essentially a prototype warframe made of Technocyte that looks like a mix between Rhino and Nyx which is worn by a woman who is working with Mezner. Nemesis infects Hayden with the same modified strain of the Technocyte virus that has infected Mezner.
At this point, most of the game of Dark Sector plays out. Hayden reacts uniquely to the virus as it only mutates his right arm/shoulder visibly. For other humans and animals, the pain quickly drives them to insanity and they mutate into horrible monsters with techno/organic parts. Hayden also has congenital analgesia which makes him not feel pain, something that most likely was one of the reasons the virus didn't drive him mad.
At the end of the story, Hayden acquires another prototype warframe (that uses the same character model as Excalibur or one incredibly similar), defeats Nemesis and Mezner (who was driven mad by the virus) and survives the traitorous Agency. Even so, the Technocyte virus ends up being released into the world either through Mezner's efforts or intentionally by the Agency.
While the virus itself is not airborn, it still spreads over the planet Earth and consumes most fauna, either killing creatures or turning them into monsters. Hayden Tenno is the only one known to have assimilated and adapted to the Technocyte virus.
Orokin Era
Flash forward a few thousand years (or potentially more). A race called the Orokin exists. They were either robots/AIs created by the remnants of humanity or a totally alien race that showed up in our solar system. For a time, the Orokin ruled the solar system and spent a great deal of time building large outposts and experimenting on genetic remnants of creatures found on Earth. From these remnants, post-humans were recreated. There were some failed experiments like the Desert Skates found in the new Grineer Settlement tileset who appear to descend from Earth's manta rays. The experiment that was the most important was the creation of the race known as the Tenno. As Hayden Tenno was 'the first Tenno', they were either created from Hayden's genes and adapted strain of the virus or descendants of his that carried the altered virus and similar genes. The Tenno were named after him.
The Tenno were unique among the new races in that they possessed a vastly superior ability to interface with technology due to their possessing the assimilated Technocyte virus. The Orokin created warframes for the Tenno to use, body armor made from Technocyte material. This gave them the ability to don the armored suits and have great power and physical enhancements.
From here, things get a bit less specific. It is most likely the the Tenno are responsible for the fall of the Orokin via the events known and referred to as the Old War which was followed by The Collapse. It is for this reason the Corpus refer to the Tenno as 'the Betrayers', as the Corpus worship the Orokin and the technology they can salvage from them.
After The Collapse, humanity split in four major directions. The Tenno went into cryosleep for unknown reasons. The Technocyte virus was either still present from its ancient days on earth or was re-released when the Orokins were defeated as much of the recreated humanity became the Infested. It is also possible that the Orokin re-released a Technocyte virus similar to the one that originally ravaged earth in an attempt to combat 'The Sentients' during the Old War. Some of the post-humans took to cloning themselves to create armies and due to a flaw in the cloning process, they took on mechanical enhancements and became the Grineer. The Corpus were certainly the most tech-savvy of the post-humans as they became a 'Merchant Cult' that worshiped money and relics from the Old War.
Warframe Era
Flash forward a few hundred years. The Corpus control most of the resources, shipping and commerce in the solar system via trade routes known as Solar Rails. The Grineer both fight with the Corpus for power and buy technology from them to support their constantly degrading bodies. The infested spread to a number of different locations on numerous planets. All that is left of the Orokin are towers in a dangerous area of space known as the Orokin Void.
It is now that the game of Warframe takes place. The Tenno are being woken up by a group known as The Lotus and subsequently, other Tenno. Most Tenno acquire or build warframes and go to work for the Lotus, acting against the other three factions in the solar system. Presumably as a byproduct of the freezing or revival process, the Tenno that are awoken have little to no memory of the past.
The Lotus is an organization that leads and organizes the revived Tenno, mostly through a female entity also known as The Lotus. It is possible that The Lotus are AI and descendants of or related to the Orokin. The Lotus emblem also adorns some warframes (such as on top of Excalibur's helmet) meaning the Lotus had to exist during the Orokin era when the Warframes were created.
References and Evidence
Origin of Technocyte/Technocyte's Properties
The events of the game Dark Sector can be read about on the Dark Sector wiki or learned by playing the game. The devs have officially confirmed that Dark Sector is canonically part of Warframe's lore.
Orokin as Genetic Manipulators/Creators
Orokin genetic experimentation was mentioned specifically during Livesteam 11 at the 31 minute mark. "When Earth got totally screwed over and the Orokin started using using DNA to rebuild different animals that suited them, some of that stuff went wrong..." referring to the creation of the Sand Skate (manta ray) enemies that appear in the Grineer settlement tileset. Their DNA rebuilding and manipulating was certainly responsible for the recreation of humanity (referred to in the story as post-humans) as well as the Tenno and warframes since living creatures in the solar system were all either dead or Technocyte monsters (infested or infested prototypes) during the Orokin age.
Official lore for the Tenno states that they are descended from a 'mystical' race on earth (Hayden Tenno and humans like him breeding technocyte-adaptable humans). It also states that this was during the Orokin Era, long after most/all of humanity was killed or transformed by Technocyte. In addition, it says specifically that it was the Orokin that created the warframes and numerous sources in-game and otherwise confirmed that the Tenno are the only ones capable of using the warframes (the Grineer have tried and the Corpus trade the ones they collect but can not/do not use them). The Tenno being related to Hayden Tenno or his ancestors genetically, being the only living creatures adapted to Technocyte, are the only creatures that can control the Technocyte-based warframes.
There are vague references by the Infested boss J3-Golem that the Tenno exist in bodies not entirely unlike the assimilated bodies of the Infested, chanting "Why do you destroy us? We are your flesh.", assuming a connection between the virus that consumes and the Tenno themselves, further confirming the notion that both the Tenno and the Infested are both products of the Orokin Era. J3 could also be referring to the Tenno flesh metaphorically, meaning their warframes.
Orokin as AI/Robots
They referred to their enemies in the Old War as 'the sentients'. This would imply that they themselves are not 'sentient' (or at least not traditionally so) yet they are intelligent enough to create advanced technology and to describe their enemies as sentient. Them being of 'non-sentient' intelligence adds to the notion that they possess artificial intelligence or are an alien race so far removed from what we know as sentient that they wouldn't consider themselves such.
In Livestream 11, at the 21 minute mark, the devs also discussed future missions planned that will take place in 'virtual space' in the Orokin mainframes. There you will do battle Tron-style with the AI controlling it, lending more credence to the notion that the Orokin were a form of artificial intelligence themselves.
Additionally, the Orokin towers we invade in the Void are filled with hapless Infested, Corpus and Grineer that entered the tower and had a computer chip-like device implanted in them which allows an entity known as the Neural Sentry in each tower to control them and use them to defend the tower and its secrets. This may have been a last resort failsafe implemented by the Orokin or the Neural Sentry to defend what knowledge it contained in case the Orokin were not around to assist in it's defense, which we assume at this point that is the case.
As a part of gameplay, Tenno can dematerialize enemies they need to capture (during capture missions) where they are presumably stored or at least transported as digital information. Such technology would be natural for the Tenno to have as they are Orokin creations and as this post postulates, the Orokin were likely digital entities themselves.
The Orokin also have no fear of the Technocyte virus as they experimented with it and possibly creatures infected by it. The only reasonable way they would not fear technocyte (a virus that can afflict living creatures) is if they themselves were not 'living'.
Tenno Being the Sentients that Ended the Orokin
The Corpus are described as worshiping the Orokin and their technology in a number of places (in-game lore, for example). They also refer to the Tenno as 'the Betrayers'. Due to the warframes (and as I have explained, the Tenno themselves) being Orokin creations, it stands to reason that the Tenno betrayed the Orokin. There is no known tie between the Tenno and the Corpus that would explain their title as Betrayers beyond that of the Tenno betraying the Corpus 'gods' the Orokin. Said betrayal would be what is considered the Old War that ended the Orokin Era (and the Orokin) and started period of time known as The Collapse.
Lotus as an Organization/AI Relation
In Livestream 11, at the 22 minute mark, the devs describe a future mission in which the player will escort 'the Lotus' (the entity) which exists inside of a kind of floating robotic drone. The drone and mission are described as you personally escorting 'the Lotus herself' and that she inhabiting the drone puts her in jeopardy.
The Lotus herself says in game at the end of some missions, "Great work. The Lotus will be pleased with your performance." As she never speaks of herself in the third person, it is safe to assume that The Lotus is an organization or group consisting of multiple entities. It is also possible that said organization is made up entirely of Lotus entities as some kind of hive mind of conglomeration and that the Lotus entity that helps you on one mission could very well be different from the one that helps you on another.
Infested Speculation
The game lore specifically mentions that the Infested come from a plague that was remarkably similar to the one from Earth's history, the Technocyte outbreak that started at the end of Dark Sector. It is likely that the Infested are the same virus or strain of Technocyte that existed on Earth in the ancient days, only its new victims are the Grineer and Corpus. It is also unlikely but possible that the Orokin re-released the Technocyte virus on the solar system (and on their newly created post-humans, the people that were to become the Grineer and Corpus) during the Old War in an attempt to stop the Sentients (Tenno) by using infected creatures to their advantage. A third possibility is that after the Old War, the Technocyte experiments the Orokin were running managed to spread on their own now that the Orokin were no longer there to control them, eventually creating the Infested.
Tenno Speculation
It is highly likely that the human-looking men and women rescued during Warframe's Rescue missions are Tenno without warframes on. Instead, they wear futuristic-looking jumpsuits with integrated boots and helmets. The only other possibility is that they are unmasked Corpus but the fact that they work for the Lotus and have Lotus symbols on their helmets makes that very unlikely.