[WARNING: Spoilers for The Last of Us: Part 2 below]
Throughout The Last of Us Part 2, the player is left to wonder what exactly happened to the Fireflies from the first installment. In The Last of Us, the Fireflies end goal was to hopefully discover a cure for the fungal Cordyceps nightmare that took over the world. Joel's journey in the first game was entirely justified by the possibility that Ellie's immunity to this infection could potentially create a cure. However, it is tragically revealed that for the serum to be created, Ellie's life must be sacrificed.
This is when the ending of the The Last of Us rears its ugly head. The player takes control of Joel as he massacres his way through the Firefly hospital to reach his newfound daughter surrogate. Joel's love for Ellie has forced him to commit a horrible atrocity that quite literally wipes out the Fireflies and removes the possibility of a cure likely ever being created. Joel is unwilling to let go of his "baby girl" even if her sacrifice would help the world at large.
The demise of the Fireflies has a huge impact on the narrative of The Last of Us Part 2. While the first game serves to demonstrate the benefit the Fireflies would have provided the post-apocalyptic world, in the sequel the Fireflies are nowhere to be found. In The Last of Us 2, during the first time playing as Abby, the player goes on a small adventure with Jerry Anderson, the Firefly surgeon tasked with Ellie's deadly surgery. He is also Abby's father. More importantly, both Jerry and Abby are members of the Fireflies. However, when Abby sees the result of Joel's ravenous attack on the hospital, including the murder of her father, she reconstructs herself completely. After this point, Abby leaves the Fireflies, and opts to join WLF with one goal in mind; to find and murder Joel Miller.
Where are the Fireflies in TLOU2?
Throughout much of The Last of Us: Part 2's story, the player is made to believe that the Fireflies are nothing more than a distant memory. Even so, toward the end of Abby's arc, she travels to Santa Barbara with Lev attempting to follow up on a rumor of Firefly activity. Shockingly enough, her seemingly unpromising lead brings her to a radio station in which she can get into contact with another Firefly. After this, Abby is invited to join them, and despite her near-death experience with Ellie, she leaves with Lev presumably to meet up with the Fireflies.
The news that the Fireflies are still out there is a huge revelation not only for Abby but for the entire TLOU universe. The idea that the Fireflies are trying to regroup to produce some sort of serum is a promising plot thread that could be explored in a potential future installment. For now, the involvement of the Fireflies within The Last of Us Part 2 narrative is somewhat minimal until the last quarter of the game. Nonetheless, the idea of the Fireflies being prominent once again in a third game is an interesting proposition to consider in the future.