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    The true Divergence 
  • Given that it's physically impossible for Nadia ("Baldwin") to be 40 years old (or so) by the time the series starts, yet both Nadias (normal and alternate) have experienced fundamentally similar events, the event in circa 1988 that essentially "duplicated" the worlds did not immediately trigger a massive divergence, especially as human timescales are relatively long compared to near instantaneous universal splits. Therefore, the true divergence of the two worlds must be at around ten years after that incident, and this WMG supposes that it was due to the built-up diverged mutations of viruses and bacteria, which reproduce on much faster timescales than humans do - and resulting in a mass disease outbreak in the alternate world, either accidentally through cross-universal contact between an immune carrier of a disease the alternate world had no immunity to, or purposely through secret biowarfare.
    • In the second episode, they said both that the divergence was thirty years ago and that it happened when Nadia was around ten. So she is around forty, even if her actress isn't. She's playing someone in her forties who looks younger than that. This is not impossible; I myself am in my thirties and constantly mistaken for being in my twenties or younger (this isn't a boast; sometimes being called "kid" by someone younger than myself is annoying).
    • It seems that everyone here is discounting the fact that while the worlds did diverge immediately, it has repeatedly stated that the divergence was insignificant at first, and in all likelyhood the cause of the divergence was the creation of the two worlds and "butterfly effect" of the two worlds' reactions to the existence of their counterpart world causing knockdown effects. So while things did change immediately, for the first decade the vast majority of divergences would likely be geographically confined to the Berlin area, with more serious run off effects taking much longer to manifest. So, the two of them could've easily had virtually identical childhoods even after the initial point of divergence for the world at large. This ia supported by the statements that when people meet their other they sometimes go insane trying to trace the exact point where things changed - meaning that the time that each "other" pairs lives changed is different for everyone.
    • The Wiki for the show, which seems to be based on Word of God, states that the 1996 flu emergence caused "The Break". Consequently it is possible that Nadia is around 30 and not 40. So not confirmed or jossed firmly as of yet.

    The Mass Disease 
  • Given the advertisement which portrays a child choking and the the other children immediately putting on masks, as well as the remarks about advanced vaccines and treatments the alternate world has developed, this WMG now proposes that the divergence had an almost immediate effect on disease mutations which triggered off a much more dangerous airborne disease epidemic (possibly Ebola), but because of the temporal proximity to the hole being made between the two worlds, the alternate world's leadership began to suspect the normal world of conducting biological warfare to "clear the path" to plunder that world's resources. Supporting the possibility that the infection was deliberate is the insistence of the normal world's diplomatic personnel on gaining geological coordinates of natural resources as well as detailed population census data.
    • Seems Confirmed as of "Shaking the Tree" (01x05) when Emily Prime discusses a mass flu epidemic in the 1990s that killed seven percent of the world's population, or between 350 and 400 million people. Such a "superflu" is comparatively rare in modern times.
    • As of "The Sincerest Form of Flattery" (01x07), it is revealed that the disease first manifested within pigs and then spread to humans. Diseases that cross species tend to be fairly rare, lending credence to the possibility of bio-warfare instead of an unfortunate mutation.
  • The theories posted here are pretty unlikely, for a few simple reasons. The reasoning behind the previous tropers bio-warfare theory is wrong, because cross species diseases ARE fairly common, at least when it comes to pandemics. Nearly all the pandemics that killed significant portions of the worlds population have come from domesticated animals, ESPECIALLY super-flus. An illustration of this is the fact that the native Americans had no such plagues prior to contact with the Europeans due to the relative lack of domesticated livestock, and were decimated by such diseases upon the arrival of Europeans. Examples of these cross species pandemics are just about any diseases referred to as plagues, and almost all the superflus that surfaced in the 20th/21st century - the most recent being the "avian" flu scare and perhaps far more relevant, the "swine flu" that was quarantined and pigs culled before it could become a pandemic that killed hundreds of millions of people. The writers likely decided it would be a swine flu that killed all those people to reference that event in real life and hint that that was the specific flu that killed all those people on earth prime, and I'd even go so far as to say it was deliberately picked to indicate that earth actual/alpha was NOT responsible for it, considering as how the same thing almost happened to us in real life. The idea of mutations of microbes being the cause of the superflu is unlikely because just a few seemingly unrelated points of divergence could've snowballed and caused the swine flu pandemic we averted in real life to fail to be quarantined and spiral out of control on earth prime. An example of a possible small divergence that could've caused it could be just a farmer that culled his herd in the real world deciding not to in Earth prime, allowing the flu to spread and kill everyone. I'd say something like that is a lot more likely than separate viral development, while being MUCH more likely than bio-warfare.
  • They refer to the pandemic as the "Munchen virus," meaning it either emerged or was identified in Munich, Germany. Cropping up in the only nation connected to a parallel universe is quite a coincidence. Theory: A faction in the Alpha universe released the virus precisely to cause a divergence, for the sake of the information trade. Info from a universe just like yours isn't of much use. Info from a universe where technological and social development took a different path is much more useful. Invasion was never on the table: the Crossing is too much of a choke-point. Using it to transfer enough troops and equipment just isn't viable.
  • Confirmed in "Twin Cities" (2x06): the Munchen virus was made by Alpha!Management, though it's still unknown whether it was released deliberately or accidentally.

    Howard Prime 
  • Given that alternate Howard is in contact with an apparent hard-liner, Alexander Pope, in his world, he could be deliberately or unknowingly subverting the normal-verse Howard to help lay the ground for an invasion or takeover attempt. Supporting the possibility of a conspiracy within the conspiracy is that he lied to Howard about "his" Emily.
  • It currently appears that alt!Howard is not part of the group of hard-liners, given who his source is (normal!Emily) and the show's reveal that his mentor, Pope, was the one who put out the hit on him.

    Emily's "nature" 
  • In "The Lost Art of Diplomacy" it is revealed Emily had some kind of past, or is an unusual person. It is possible, given her apparent age of between 45 and 55, to suppose that in her teens or twenties she may have been a prostitute, to which she assumed Howard would take exception and so never revealed that information.
  • Given how well-off her family is, prostitution seems unlikely. She wouldn't have hurt for money.

  • We haven't seen him at all in Season 1, and there's probably a reveal waiting in Season 2: he's one of the chief hard-liners on the Prime side.
    • Or he's long dead of the virus.
    • He's revealed in season 2 to be a prisoner in "Echo," a facility where people are kept for interrogation in the hopes that this will ultimately reveal useful information about their counterparts.

    The Hard-Liners' Plan 
  • The natural revenge for the Munchen Virus is for Indigo to release their own plague in the Alpha universe. If they did, Alpha's best hope would be Prime, which has more advanced medical technology. Getting in the two sides to break off contact was the first step in that plan.
  • Confirmed in "In From the Cold" (2x08): Myra wants the Alpha and Prime universes to go their separate ways, but first she will release the flue virus in Alpha 'to restore the balance.'

    The Crossing 
  • Prime has either found a 2nd Crossing or invented a way to send agents over. This is why they have more spies.
    • There does appear to be a second crossing between the interface rooms, confirmed in the final episode(s) of the second season. I think that's more just a plot hole though.
It will be revealed there are several crossings
This would explain the ‘illegal immigration’ sub plot, as well as the fringe groups successfully replacing so many Alpha world people without Alpha border security realizing that a number of them are out-staying their visas by years and decades.

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