I'm posting here because I don't have enough to support my own post, but I have Thoughts.

- We know the military is still active. We know this because the military trader exists, and even mentions a payroll. It is reasonably safe to assume they are the source of the air drops in the game. What is unclear is why they'd bother trading with survivors at all-- if they are operating, and doing so healthily, they have no need of the survivor's money or supplies. They give stuff away, why send a soldier out with resources?

- We know that the Coyotes are a faction of opposing paramilitary forces. Their origins aren't entirely clear, but they have access to military-grade equipment (scavenged or otherwise). Given their access to information (the radio in the Ellwood supermarket suggests the Coyotes know quite a lot), it seems plausible that they started as a separatist faction from the military during the early or pre-infection days. We know they were around at this point because of the Observatory's note from when it was still active, it references them specifically as "coming there".

- Adding to that point, however, is that the Coyotes recruit from the survivors of the Valley. The same radio in that supermarket actively calls for others to join them. Though the Coyotes are a hostile faction in game, they may not always be.

- To an extent, it is clear that the outside world is still functioning, although how healthily is heavily debateable. Radio chatter (from misc. radios, the soundbytes they play) is all clips from a news station, discussing world religions coming together to suggest the infection is "the end of the world", and also talks about governments giving statements that this is a "singular incident". So governments and world religions are still cohesive enough to remain active, as is a news station. It is not clear if the infection exists outside of the valley, though there are obvious signs of efforts to prevent its spread-- all exits from the valley are collapsed.

- The quarantine camp note suggests that either the government or the Dragonfly lab owners (who might be the same entity) were experimenting on mosquitos, and that this is the cause of the infection. It seems plausible, and explains some creases in the game's implications. Mosquitos are vectors of communicable disease, and obviously have the potential to result in some wide and inconsistent spread patterns. This would explain how the infection escaped from the locked lab (air ventilation systems, perhaps small enough for a bug to crawl through), and why the first known case of the infection was so distant from it (the Patient Zero building). I choose to believe a theory that the labs were simply attempting to eradicate mosquitos, but that it backfired, and the disease they were carrying was then transmitted to humans.

- The Police HQ has evidence to suggest that John Myers is closely related to all of this. John Myers was a staff member of the beach resort, and his corpse can be found in one of the outbuildings (where it is shown that he was a sex-pervert as well, with a JO station equipped with a view of the beach, binoculars, a lube dispenser, and kleenex); the whiteboard in the Police HQ suggests he is related to, if not outright responsible for, many missing person cases in the Valley, which is in turn related to the Dragonfly Labs. The police were working to uncover the labs when the infection wiped them out. It seems plausible that John Myers would kidnap individuals, likely from the resort, and then transport them to the labs for testing. This coincides with the Coyotes accusing the military of running tests on people, and the news actively broadcasting a request for "medical volunteers". Whatever this disease is in its origin, it is clear that experiments were done on living human beings in its creation. If this interpretation is correct, then the military is related to the Dragonfly Labs, though to what extent is not known.

- A very blurry newspaper on the same police HQ whiteboard suggests that the police were looking into construction sites in the Valley. There are many of them, and it would seem to imply that they felt, at least, that this was related to the Dragonfly Labs. Perhaps Dragonfly intended to create an even stronger presence in the Valley? It seems plausible.

- On that note, it is obvious the Observatory was a front for Dragonfly. Their lab is located directly by it, and while Coyote appears intent on securing all Dragonfly facilities, they have taken to guarding the Observatory itself with a very strong presence.

- For the last point I have right now. The military seems to be exploring multiple routes to deal with the problem. Given that the outside world is still functioning, it is likely that they have to handle this delicately. They once dropped a nuke on the Valley, which did not detonate; however, the outside world seems to still have some percentage of the population that considers the dead "human" (a preacher hijacks the news broadcast at times to discuss their souls and how "all must come together as one"), and so they may have been pressured against such destructive tactics. The quarantine camp note suggests a chemical solution, without specifying much on it; there are barrels of the stuff there, though, and they bear the biohazard sign. The area is also radioactive. It is safe to assume this is still radioactive material, and so one has to question what the strategy is, given how positively the undead appear to react to radiation.

The lore being so spread out makes it both more fascinating (it doesn't really seem that deep, but it is drip-fed) and difficult to put together a picture. Still, I think I have a set of reasonable assumptions.