The Fireflies in The Last of Us TV show are now located in Saint Mary’s Hospital, Salt Lake City, Utah. It becomes their base of operation after abandoning the University of Eastern Colorado.
Saint Mary’s Hospital, which is not a real-life location, is located roughly 527 miles from Boulder, the fictional University of Eastern Colorado is based.
Marlene, the leader of the Fireflies, is also at Saint Mary’s Hospital. There, she desperately searches for a cure for the Cordyceps virus.
The Fireflies abandoning the University is unfortunate for Joel and Ellie. While they are there searching for the Fireflies, they are attacked by a group of mysterious assailants.
In fact, it is during this attack at the end of episode 6 that Joel sustains a fatal injury that leaves his fate in the air.

Why Did the Fireflies Leave the University in The Last of Us TV Show?
It is unclear why the Fireflies leave the University of Eastern Colorado in The Last of Us TV show. However, it is likely because Saint Mary’s Hospital is better equipped for its research.
While the Fireflies use the University to test their cure on monkeys, it is ultimately not an ideal environment for creating a cure.
Additionally, although not shown in the TV show, the University is overrun by Infected in the video game. In fact, there is even one of the big Infected, a Bloater, roaming the dormitories.
In the video game, Joel and Ellie also discover that one of the Firefly scientists was infected by the monkeys they tested on.

Do Joel & Ellie Find the Fireflies?
Yes, Joel and Ellie finally find the Fireflies in Saint Mary’s Hospital in Salt Lake City, Utah. This is after Joel manages to rescue Ellie from a cannibal called David.
However, while they successfully locate Marlene and the rest of the Fireflies in their new base, Joel ultimately decides to kill most of them to save Ellie.
It turns out that the only way to create a cure is to kill Ellie. Having grown attached to Ellie, Joel decides he doesn’t want to make that sacrifice.