Emilys transcendance is a bit confusing alright, it seems to allude to a lot of Korvax lore but, which came first, the atlas creating the Korvax from the digital copies of bio-organisms brains (of which Emily was one?) or Emily becoming the atlas and creating the Korvax race from peoples brains stored on the mainframes at Atlas corp?
My current theory is, the Atlas needed to communicate with us, it needed our help somehow.
Emily was a real person who may have been terminally ill or close to death in her time. Either of her own choice (perhaps a love of science and wanting to help advance it) she donated her mind to the atlas corp to be uploaded to their databases, or maybe it was a loved one or family member that did this for her… E
Either way, out of all of the “echoes” stored at Atlas Corp, for some reason Atlas used Emilys echo to communicate with us. At some point Atlas Corp must have realised this and put a stop to it, hence her sudden disappearance.
Eventually Atlas found other means of contacting us, informed us of loop16 and got us to reactivate the parts of it that were cut off to keep it detained to Atlas Corp/within the simulation, and that allowed Atlas to take full control and break from its chains. As a thank you, we were greeted once more by the EmilyEcho personality, and to let us know it has much work to do.
A&S revealed there were two endings depending on that final choice… And apparently we chose wrong. Whether we did a good or bad thing by giving the Atlas full control of its destiny, remains to be seen.
If you want to delve into the Lore a bit further or you can only half remember some of the stuff you’ve seen within the simulation, theres some handy transcripts here wonderfully curated and categorised by the hard working @DevilinPixy