With her immunity, Ellie might have provided humanity with a new hope to overcome the Cordyceps infection. The outbreak, which led to the destruction of the modern world, causes its victims to succumb to a putrefying fungus which grows from the inside of their bodies and out. However, the fungus begins its hold on the infected by growing all over the brain. As a result, if the Fireflies extracted it from Ellie, it would have killed her. Joel’s choice to stop the procedure and lie to the girl about what happened in that hospital is one of the most controversial in gaming.