The Last Of Us 2: 11 Perfect Theories That'll Blow Your Mind
3. Joel Killing The Fireflies Is What Allowed The Cult To Find Ellie
With the theory that Marlene spent her time in the Fireflies using her resources to keep Ellie out of the cult's clutches in mind, it's been theorised that Joel murdering them all at the end of the first game could have opened the floodgates for the religious fanatics to catch up to her.
There's no way Naughty Dog is going to let Joel get off scott-free with his actions from the end of the previous game, and if he inadvertently put Ellie in danger because of his own selfish desire to not lose her, it would have huge ramifications on their relationship going forward.