The Last Of Us 2: 11 Perfect Theories That'll Blow Your Mind
2. Ellie's Link To The Fireflies Will Complicate Joel Murdering Them All
Even if Joel's actions at the end of the first game aren't what cause the cult to realise Ellie is alive, they're still going to come into focus when Ellie realises just how tied to the Fireflies her mother really was.
Hell, it's not even guaranteed that Anna is definitely dead, and instead of sacrificing herself, the character could have just gone into hiding so the cult thought they'd killed her, unable to communicate with Ellie in fear of putting her in danger.
Consequently, Joel murdering the Fireflies could be what brings her out of exile, with her mission becoming complicated when she realises that the person responsible for killing her best friend is also her daughter's guardian.