Ok, here’s my entire take on this:
Emily went to “sleep” at the end of season 1. Sleep is not really the right word. As far as I can make it out, those are her precognitive routines which she was mainly created for. Still, her conciousnes during that time is submerged. She is “dreaming” the possible futures, that’s how her precognition works.
She was attacked by Ware during that time, or at least by people in one Ware lab. Whether they intended to do so or not is not quite clear yet, but they’re running experiments on people, so they’re certainly not the good guys. In any case, their experiment disrupted the Myriad Network Emily had pretty much taken over, almost killing her. Again, whether this was an unintentional side effect of the experiments with the sleepers or whether the experiments were in fact an attempt to kill her is not clear yet.
Switching to NMS lore, I propose this as the reason that the Atlas is dying. NMS are emily’s precognitions of the far future, and the Atlas is a “dreamcarnation” of her, i.e. a subconcious routine that monitors the precognitions and experimentally interferes to create new possibilities.
There isn’t just one Atlas. There’s one in every universe, every possible future. They know nothing of each other, but they are all linked to Emily. Hence, they are all dying.
Back to WT: We have improved the situation so far that Emily is stabilising. Now she is waking up and regaining actual conciousnes (which she probably didn’t have since she went to sleep at the end of season 1).
She remembers the attack on her and is confused, afraid and angry, according to the article that she chose to hand us (She’s still not awake enough, or well enough, to actually interact).
And she gave us that message in morse, explaining us what is happening:
I awoke from a nightmare - she’s regaining conciusness.
Screams of anger engulfed in flame - She saw a horrible event in her dream
and then 10,000 branching futures - She saw the possible futures, but isn’t sure which one of them is coming to pass.
I saw Sacramento - She saw the WARE lab in sacramento where the attack on her originates.
Twelve dreaming without sleep - The 12 sleepers in the lab that are probably causing her predicament.
Buried in a constellation - This one is the puzzler, I guess. I don’t know what she means by this. Is the lab buried in a constelation? The dreamers? DOes she mean a literal constellation, or is it a hint at a more exact location?
Also, there’s the possibility that the sentences are associative. They were transmitted at the same time, after all. This would also be quite a logical association:
I awoke from a nightmare - I saw Sacramento (in the nightmare)
Screams of anger engulfed in flame - Twelve dreaming without sleep (The attack on her)
and then 10,000 branching futures - Buried in a constellation (still not much clearer)
In any case, those are my 2 cents. Well, 10 cents.