After everything they’ve been through, including facing very dumb cannibals that refuse to just eat the mushrooms off the infected, Joel and Ellie reach Salt Lake City, where they are taken by the Fireflies. There, Joel finds out that, in order to make a cure, the doctors have to cut up Ellie’s brain, which causes him to go berserk and kill almost everyone before escaping with an unconscious Ellie.
Once Ellie wakes up, she asks what happened. Joel lies to her, saying there was no cure and raiders attacked the hospital, conveniently killing everyone. Even when she presses him on it, Joel doubles down on the lies and swears he’s telling the truth. This, of course, messes Ellie up. For her, a cure would mean her journey was worth it, worth the pain she went through and worth every death, from Tess to Riley to Sam. She knows that, if Joel is lying and there was something else to what happened at the hospital, it means he did not respect her wishes.
This exchange is the most heartbreaking part of the finale, a moment that changes everything. Even if we don’t see them fight or see Ellie walk away from Joel, Bella Ramsey’s acting makes it clear Ellie is aware Joel is lying. How much of the truth she knows or can imagine is left up to interpretation, but in the final moment of the season, when Joel doubles down on the lie and Ellie just says “Okay,” in resignation, it is clear their relationship is forever changed. Something broke in that moment that isn’t easy to put back together.