Someone mentioned coming up with a better plot. CHALLENGE ACCEPTED.
How about this one? We've already established Ellie's immunity is symbiotic, not just 'fuckoffspores'.
Here's the jump: what if humans with said symbiosis can start influencing or controlling the zombies? Yeah, I'm lifting a bit from Starcraft here; but here's where things get fun and creepy:
Ellie's not the only 'symbiote' out there. There's one (let's call him Karl) who's gone a BIT further along the tech tree for 'take control of zombies'. Why aren't there as many zombies around? Because Karl's snatching them up, 'programming' them, and putting them to work. He's not out to rule the world, but he's trying to rebuild his corner of it, and it's dawned on him that he's going to need help. Not just extra hands, but the symbiotic genes need to be passed down.
And lo and behold, there's young, reasonably nubile Ellie.
What follows is probably one of the most deranged three-way chase scenes in a video game. You still have Abby (who is either a guy or a girl, PICK ONE FUCKER) trying to track down who killed her dad for revenge. You have Joel and Ellie just trying to get the fuck away. And you have Karl who is trying to bring Ellie in so he can sire more symbiote-humans with her. He'll happily cut a deal with Ellie -- heck, Karl could use a guy like Joel on his side -- but he's absolutely convinced that humanity can't just shoot and burn its way out of this mess, and that they need to 'spawn more overlords'.
Yeah, I know, sounds like fetish fuel, but probably still better than what Dumbfuckermann puked onto the disc.