Joel and Ellie go around campus looking for the Science Building on horseback, which according to Tommy looks like a "giant mirror". Ellie names the horse Callus, since they forgot to ask Tommy for his name. As they search, Joel starts to share a bit more about his past, telling her about his childhood dream to be a singer and how he never got to go college for being a father so young, and talking to her about football. He goes off on his own at one point, passing through a dormitory filled with infected, in order to reach the generator that opened a locked gate. They start to realize how strange it is that the place is completely deserted and that they should have seen someone by now, since the only thing they encountered was a group of monkeys running around in a square near the dorms. He speculates optimistically that the large number of infected is used by the Fireflies as a defense mechanism, as Bill did.

As they enter the Science Building, they realize that the Fireflies had left in a hurry, for reasons unknown. Joel finds a recorder near a corpse of a Firefly scientist, and learns that they were using monkeys as test subjects, trying to study the effects of the Cordyceps Brain Infection in order to find a cure. The scientist, who had been instructed to kill the infected test subjects, instead believed they deserved to be free. While trying to let them out of their cages, he is bitten by one, subsequently passing the infection onto him.
During a cutscene, another recording reveals the Fireflies have gone to Salt Lake City, Utah, to continue their research. After they discover this, a group of looters ambush them. Joel and Ellie make their way through the building, killing their attackers as they go. Joel is caught by surprise by one of them, when they burst through a door he's opened. They struggle briefly, before Joel punches him the looter, however, brings Joel down with him, and they both fall off the balcony together. The looter dies on impact, but Joel is impaled on a metal rod shooting up from the ground. Ellie climbs down and helps him to his feet, and guides him towards the exit.

Ellie is forced to protect the both of them, as Joel is incapacitated by pain, and extreme blood loss. They manage to exit the building and, after Ellie shoots a looter who attempts to steal Callus, ride away from the university. Joel taking the reins, they get far enough for Ellie to assume they are safe. Suddenly, Joel slumps and falls off the horse, passing out. Ellie tries to wake him up, calling his name and asking him what she should do.

The season ends with the screen fading to black.