This is my spoiler-free speculation:
They're at the University of Colorado, and are exploring a seemingly abandoned science building. I believe they will manage to find some living scientists, otherwise this cross-continental journey would have been for nothing. (And I am still working out how they made this journey post-Pittsburgh. I assume they jacked cars here and there. I don't believe they could have done it on foot. The time skip between Pittsburgh and Jackson was jarring. Am I supposed to assume the months between were uneventful?)
Anyhow, this game has been bleak, but so far it hasn't been crushing. Thanks to some characters still being alive at this point, this game hasn't reached Walking Dead levels of despair. However I think it is unlikely that both Joel and Ellie will survive the conclusion.
Joel thinks that scientists can draw some blood from Ellie and make some type of vaccine from it. Um, Cordyceps is a fungal infection. I am not aware of any fungal vaccine existing outside of early testing phase in real life. But ok, I can roll with that. I hypothesize they'd want skin samples - and considering where the fungal parasite migrates in the body - they'll want to study her brain. They'll sacrifice her and extract her brain in order to determine why the parasite didn't latch on.
I suspect there are two possible endings. One will be the "bad" end, where Ellie dies, a treatment/cure is developed, and Joel has to live with the guilt of leading her to the slaughter. Then there is the "good enough" end, in which Joel dies protecting Ellie, and somehow Ellie can contribute to the development of a treatment/cure without losing her life. And yes, both of these sound unimaginative, but the game's plot has been straightforward with no curveballs. One has to be coming.
Something has to be up with the Fireflies. Maybe the Cordyceps mutation was engineered as a bioweapon. Too Resident Evil, and it's a poor choice for a bioweapon. Or maybe Elly is harboring a different variety of Cordyceps.
Ok, less type more play.
Is there a point to collecting Firefly tags?