The Last of Us Episode 9 Recap: What Happened
Joel and Ellie reach the Firefly hospital. Joel learns that the vaccine will kill Ellie, so he kills everyone in the facility to save her and lies to her about it afterward, ending the season on a note of tension.
The Hospital Massacre
Upon learning that the Firefly doctors must remove Ellie's brain to create a vaccine, Joel's parental instinct overrides his morality. He launches a one-man assault on the hospital, killing soldiers and doctors with cold efficiency. He rescues a sedated Ellie and kills Marlene in cold blood, ensuring that no one can ever come after them again.
The Final Lie
As they drive back toward Jackson, Joel tells Ellie that the Fireflies had found dozens of immune people and were unable to make a cure. He lies to her face to protect her from the guilt of her own survival. The season ends with Ellie asking him to swear he's telling the truth, and his answer seals their destiny.
Episode Cliffhanger
Joel says 'I swear,' and Ellie says 'Okay,' leaving the audience to wonder if their relationship can survive the weight of his secrets.