Saint Mary's Hospital in Salt Lake City is the Fireflies' main base and lab, the destination of Joel and Ellie's whole journey. You fight through it in The Firefly Lab, the last full chapter, which has one section, The Hospital, and 5 collectibles.
Fireflies find Joel and Ellie in the city, knock Joel out and bring both into the hospital. Joel wakes in a hospital bed with Marlene beside him.
Marlene says the surgeons need to remove the fungus from Ellie's brain to make a vaccine, which would kill her. Joel kills his guard, Ethan, fights through the floors to the operating room, kills the head surgeon Jerry Anderson there and carries Ellie out. He shoots Marlene before driving away.
Boston
Boston, Massachusetts is the first region after the time skip and the city where Ellie grew up. You play The Quarantine Zone and The Outskirts here, and Left Behind's flashbacks with Riley take place in the same city. FEDRA holds the North End as one of the last working quarantine zones in the country.
Pittsburgh
Pittsburgh, Pennsylvania is a former quarantine zone now run by hunters who ambush anyone passing through. Joel and Ellie spend two chapters here, Pittsburgh and The Suburbs, and meet the brothers Henry and Sam. Expect heavy human combat and the largest pile of collectibles in the game.
University of Eastern Colorado
The University of Eastern Colorado is the Boulder campus where Joel and Ellie expect to find the Fireflies in The University chapter. You search it on horseback and on foot through the Go Big Horns and Science Building sections, and it holds 17 collectibles.
Logan James Bus Station
Logan James Bus Station is the abandoned Salt Lake City bus depot that Joel and Ellie walk through in the Highway Exit section of Bus Depot, on their way to Saint Mary's Hospital. It leads to the scene where Ellie spots the giraffes.