Are you really daft enough to believe that a person immune to the cordycepts fungus, is just going to grow old and accept a mediorce life? That her story "has concluded and there isn't much more to tell"? Ellie has no clue how to live in peace, that's what Joel has failed to understand about her if any thing. She isn't his daughter. She is a product of the plague and has no control over her own desires to explore and take risks. She's a hard ass at the core, and Joel is going to die for her mistakes.
Let's just think for a minute about the prolouge when the soldier was given orders to execute Joel and Sarah. Maybe the commander is still alive, and has his own function in the sequel. Someone who has the ability to grant soldiers the right to kill civilians is probably a high ranking person and knows what the hell is going on. Joel would give his left and right nut to murder that SOB, and I hope the government is the main protagonist in the sequel. Perhaps Ellie isn't the only one and the'yre rounding up every person immune for testing.
I know for a fact that there will be a sequel with Joel & Ellie, because Naughty Dog has a great history with things like this. Uncharted could have also ended at the first game, yet it's coming up to its fourth release. I'm going to laugh at all nay sayers, who condemn the thought of a sequel, but will be the first people to pre-order it/praise it/and again condem another sequel. It's going to come, the story isn't over. There is so much more to Ellie and Joels story that I could literally sit here and write out a thousand plots worth telling. Naughty Dog already has, and I know it's already in its infant stages of writing if not production.
I'm pretty sure the sequel will be about the government finding out about Ellie's existence, Joel finding out the moron who killed his daughter, Tommy doing something that completely betrays Joel, Ellie addressing Joels lies, pissed fireflies who (the ones who survived on the top floor of the hospital) will round up the remaining soldiers on the hunt for Joel, Joel and Ellie being in the middle of the fireflies, military, and infected.
Seriously, who ever said this story was over has no imagination whatsoever. I'm laughing my ass off at the fact that some of you really believe the crap Druckmann is saying (50/50 my effing ass), when he specifcially lied about being able to play as Ellie before the games release. It's a marketing ploy, and a smart one at that. But a ploy nonetheless. He doesn't want to give out too much information but it is coming, and the smart fans are making sure they have at least $60 to their names.