I noticed that the email says, During the boot sequence, we discovered an incomplete dataset.
That dataset led to scrambled communications from NMS. It makes me think that the Atlas Foundation doesn’t know as much as they pretend to about the system they are running. Where are these datasets from? A different timeline? A future timeline? Is this a simulation which has already gotten out of control?
Have you typed whois themis and whois metis yet? Elizabeth Leighton’s name isn’t Elizabeth. There are theories that the Top Secret correspondence reports aren’t going from different person to different person, but different timeline to different timeline. Multiverse perhaps?
Twins perhaps?
There is definitely an Elizabeth Leighton; she’s the one who livestreamed to us. Who Sophia Leighton is, that’s up for debate. Could be alternate timeline, a mother/daughter, or even data corruption in the AI’s memories.
My point was that these datasets don’t seem to be coming from Atlas Foundation, or at least not Atlas in our present time. Perhaps like other machine learning AIs, loop16 has become a black box to them, running a simulation that they don’t really understand.
The first part of phase two was “Boot Sector”. The note makes it less clear, but maybe the hex data from that part will be used later on?
http://bootsector.wakingtitan.com/
Edit: Sorry this post spins off of the timeline considerations and do not mention anything about datasets. Give me a shout if you feel it’s off topic, as I don’t wanna be “that guy”. 
All we know for sure is that
(1) Elizabeth and Sophie Leighton are not present in the same timeline, since they both claim to be CEOs of Atlas (or that they are not active within Atlas at the same time).
(2) Dubois and Elizabeth can communicate with each other, at least through written memos (first pdf from phase 001), which suggests that Elizabeth and Dubois share timelines and multiverse branches, and are acting as a team. However, the whois commands contradicts this, since they answer Dubois and Sophie Leighton, as if these two would be working partners.
This leaves us with one of two possible options imo:
(1) Dubois and Sophie Leighton belong to the same timeline and Elizabeth does not.
Elizabeth found a way to “live stream” from the future, using echo technology to be tapped into our timeline in “real-time” so to speak. She could then see our comments in the chat and answer them as well, and for all practical purposes nobody could see that she’s actually not in our time. Her previous video attempts arrived garbled and segmented since it took some time and research (in the future) to try and “live-stream” to us directly without loss of data. In the future, Superlumina messed something up that is now affecting us “in the past” (from her perspective).
(2) Dubois and Elizabeth belong to the same timeline and Sophie Leighton does not.
This makes the memo-pdf correspondence more probable, but doesn’t explain why wakingtitan dot com answers the whois commands the way it does. Therefore, under this assumption, there is something really fishy going on with waking titan overall, since the same computer (that we just booted) fails to identify the correct CEO of atlas.
We could also have situations were Sophie Leighton, the mother, works together with Dubois in our timeline, but dies or disappears and is replaced by her daughter Elizabeth, which carries on her mum’s mission and subsequently reaches out to us “in the past”. Or the other way around, that booting waking titan (something that happens in our timeline) enables the daughter Sophie Leighton to continue the mission that her mother Elizabeth started with Dubois.
And/or combinations thereof. Including my spinning head. My god I’ve been immersed in Waking Titan for so many days on end!!! Aarrgggghhhh !!!
Thanks for your thoughts on the timelines. It scrambles my noodle just thinking about it. This topic is not so much about Elizabeth and Sophia and Dubois, but more about these datasets containing transmissions from what seems to be No Man’s Sky, and what they are doing inside the Atlas system.