On the night of April 28th 2034, Joel wakes up in a hospital bed to find Marlene welcoming him to the Fireflies. After apologizing for the bump on the head, Marlene asks how Joel and Ellie managed to find the Fireflies, to which Joel responds that Ellie "fought like hell" to get here. Joel asks to see Ellie but Marlene denies him, saying that she is being prepped for surgery as they speak. Marlene reveals that the Cordyceps in Ellie's brain has somehow mutated according to the doctors, hence why she is immune. Studying the brain would allow the doctors to reverse-engineer a vaccine, though since the fungus grows all over the brain, Joel figures out that Ellie would be killed. Foreseeing this, and knowing that Joel had formed a close bond with Ellie in the past year to the point that he would not allow the surgery to proceed, Marlene orders Ethan to march Joel out of the hospital and kill him if he tries anything. Marlene leaves, and Joel, after seeing his backpack, disarms and tortures Ethan to tell him where the surgery room is. Finding out that it is on the top floor, Joel shoots him dead.
Alerted to the gunshots, the Fireflies find Ethan's corpse and proceeded to find and kill Joel. Determined by the player, Joel evades/kills them and blocked off the West Wing access. On the top floor, Joel finds several recordings, one being the head surgeon's assessment of Ellie's immunity and two others recording Marlene's indecision and reluctance to kill the child she promised to look after. Joel eventually finds the surgery room as more Fireflies guarded the hallway leading to the operating room. After killing/evading them, Joel bursts into the operating room, where the doctors were surprised to find him. The head surgeon tries to prevent Joel from taking an unconscious Ellie by blocking his way but is killed by Joel. Leaving the two assistants to their fate, Joel carries Ellie away as more Fireflies close in on him. He manages to get to the elevator and reach the parking garage but is confronted by Marlene.

Marlene attempts to reason with him, asking how long Ellie can live safely without being killed by Clickers or raped and murdered by hunters. Joel disregards this saying that it is not Marlene's choice to decide but unsure if it is what Ellie wants. Marlene allows him to live if he gives Ellie back to the Fireflies and slowly puts down her gun as a sign of trust while walking towards him. Joel hesitates for a few moments, before he shoots her with a hidden pistol. After he places Ellie in a car he walks back to Marlene, who pleads him to let her go but Joel kills her stating "you'd just come after her".

As Joel drives out of the city, Ellie wakes up, wondering what had happened. Joel answers that they'd found the Fireflies. He goes on to say that there were dozens of people who were immune like Ellie and the Fireflies were unable to develop a vaccine from them, to the point that they've stopped looking for a cure. Ellie sadly rests up while Joel takes them back home and apologizes.