Ellie overhears Joel saying he wants to leave her with his brother, Tommy. He lacks the confidence to escort Ellie to the Fireflies.
Upset, Ellie ran away
Ellie and Joel have a falling out over the situation. After learning Joel lost his daughter, Ellie tries to sympathize with his loss, until Joel says, "You have no idea what loss is"
20 years after the start of the epidemic, Joel meets a Firefly named Marlene who pays him to smuggle Ellie to the Fireflies. While making their way, they're stopped by soldiers who can scan them for infections. Before the soldier can read Ellie, she attacks them. Joel picks up the meter that says "positive." Ellie tries explaining that her bite is old. Joel doesn't believe what he's hearing until he sees her in a room with spores and she doesn't get sick, and when Tess was bitten on their way, and she reveals it at the first drop-off.