I think Sophie is the evil one and had Elizabeth bumped off, I also think Sophie is in cahoots, or at least is interfering with WARE
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Makes perfect sense to me, although I feel that Emily is not necessarily a threat in that sense. With Major Sophia Dubois being military, it makes more sense that Emily is standing in the way of military plans. W/ARE technology would likely be perfect for military use. So who owns those other labs we never heard about until recently?
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She was chief of security at Atlas, not military, as far as I understood it. I also got the feeling through season 1 that she was kind of Elizabeths right hand, so her taking over doesnât surprise me too much.
What did surprise me a little is that she doesnât appear to be looking for a replacement for Elizabeth, but for her old job. She might have her reasons for that, but Iâm not sure sheâs the right person for the jobâŚ
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Oh yes, I agree that she is likely not the right person for the job, but it does make sense to take over for the time being. Just look back at the time where Emily took over the full Myriad network, with JJ Wong going crazy. Sophia would have made different decisions, telling Elizabeth to stop the whole project. We have to thank Elizabeth for making the tough decisions needed.
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Sophie Dubois is a member of the Pentagonâs Titanwatch Task Force. Sheâs employed by the US military, and is currently on attachment to the Atlas Foundation. Supposedly sheâs overseeing the Foundationâs use of government funds, but really sheâs reporting back to the Pentagon on the security implications of Atlasâ work.
In peacetime, the government canât just take control of a private company. Theyâd need to pass laws, or emergency powers, in order to do so.
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Huh⌠if sheâs a government employee, then yes, her taking over the company is highly irregular.
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whois themis
Major Sophia Dubois,
on assignment with the Atlas Foundation.
So a military in mission. DOD propably financed Atlas for a (big) part, thatâs why Elizabeth wasnât in position to refuse an officer on assigment in Atlas.
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I think there is a distinct possibility of this being coup at the Atlas Foundation and W/ARE may actually be in charge (pulling the strings as a puppet master). There seems to be a lot of new found cooperation mentioned in that memo.
And R.I.P. Elizabeth. You will be missed.
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The lyrics to this song do stand out
Itâs the terror of knowing what this world is about
Watching some good friends screaming 'Let me out"
This reminds me of the early vids from Elizabeth, all glitchy and asking What if we have tried this before? It also reminds me of the Artemis quest. Will he be happy in the simulationâŚanswerâŚas long as he does not know he is in a simulationâŚ
So I agree with the idea that the vids of Elizabeth were echoes only she and others there have realized they are not in the real world�
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So the question is "who send mails to us ? " Who is Oldgods in the Atlas foundation ?
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You guys make me think we might not actually have woken any Titans yetâŚ
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So I noticed that the first explosion occurs immediately after Elizabeth says âFrom your friend at the DoD? This isnât under their jurisdictionâ. Maybe thatâs not what Sophie wanted to hear? Or maybe sheâs not talking to Sophie?
Also, am I the only one who thinks Atlas has been suspiciously absent recently? I mean, weâve been working for WARE for a while now, not Atlas. And why was it a Myriad team that âbreachedâ the WARE site? Why not an Atlas team? They obviously have military support, you would think that would be a simple task. If Emily really is that important to Atlas, why arenât they taking a more active role in saving her? Is Atlas really putting the fate of Emily in our hands alone?
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âAll dead?
All of them?
Sophie, this-- this changes everything, this completely changes the game.
Yes.â
She may not be talking to the Sophie, but sheâs definitely talking to a Sophie.
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Sophie works with the Pentagon and is on assignment with Myriad. Elizabeth was the head of Atlas. Both were working with Myriad and somewhere WARE was brought in. But, we know someone was misusing the WARE tech (according to Mr. Zheng) and now Sophie is in charge of everything. One person in charge is never a good thing. Who is she answering to if not the Pentagon? We have been led to believe that WARE is bad but now Emily says we must save it. WARE has also agreed to free up resources for Emily. We now have the task of integrating the 12 test subjects into the Satcom interface.
I believe this is where we now stand.
I now have a question about what facility actually blew up and why Elizabeth was there. It was obviously not her office since the Atlas Passes were found there.
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Oh, please God, no. The American military is in control of Atlas?
Weâre all doomed 
@sheralmyst this is kind of my point. Where is Atlas? They donât seem to be taking any active role in the whole Myriad/WARE incident. If Emily, a fully self-aware artificial intelligence, really is the âfuture of mankindâ as they so claim, why are they not doing more to secure it? Why are they leaving such an important task to us âkidsâ at the CSD?
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Normally that wouldnât scare me that much, since the american military is generally a lot more competent than theyâre given credit for, but right now that would mean that Trump controls Atlas. 
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Possibly why Emilyâs mental powers have all but disappeared.
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Well, in the memo found with âwhois harryâ we can read:
Cpt. James Harry, has been obstructing access to critical Myriad infrastructure. Technicians have repeatedly emailed Cpt. Harry to request access to portions of the satellite network
So it is a Captain, in Myriad, who has been obstructiong access to Myriad infrastructure; But who were the technicians ? We have 2 names:
Sgt Lyel
Sgt Klein
2 Sergents ? Wow, atm is there any civilian in Myriad ? Oh, they have an assault team able to make breach in W/RE lab too. This Atlas foundation branch, normally known for ânetwork and storage solutionâ looks like a milatary one.
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