I think Joel will be killed as a payment for his sins. I mean, he has the violent pass, he killed the innocence as a means of survival and he looks to saving Ellie as a chance of Redemption. Honestly, I'm with the rest of everyone else. Joel will probably die. There may be a segment dedicated to play as Ellie to make the final push towards your goal, barely making it. But that's too simple an ending, and I think they might leave it open for a sequel, where you play as grown up Ellie (Yay! we can beat the snot out of her now! ) and it could be role reversal, as in Ellie has to care for a little dude. But ND don't do that with their endings. However, who's to say they won't start now? Anywho, Sony will likey pressure them into making another.
1. Joel is doing this mission for a dying/dead friend, Joel delivers Ellie to her destination and the friend will be there and possibly kill Joel, Ellie will then kill this person for her bond with Joel was better than the friend.
2. Joel discovers the reason his friend wanted Ellie at this place was to use her to stop the infection, because her DNA won't allow here to get it. Joel then has the choice to either save Ellie (the process of exracting her DNA will kill her) or leave and know the infection will stop. (Save one life or save billions)
3. The military want Ellie (They might want her for her DNA). They take her away from Joel and in the last parts of the game you're all alone infiltrating the military HQ to save Ellie, you are too late, and Ellie has been killed, then Joel is spotted, and killed as well.
4. Joel and Ellie make it to a place where the infection can't spread and accidentally bring the infection there. They escape with their lives and find refuge in another area that also crumbles from infection, Joel and Ellie then die in the rampage.
5. Joel finds out Ellie will die if he brings her to the drop-point so you hold up in an abonded town and the military/bad guys start invading to get to Ellie. Joel stops them and they find a quarentine zone to live in.
This is the ending I've though up, but it's pretty sad. The military are after Ellie for some reason (I'm 90% sure of this) and want to stop her from reaching the destination. Joel and Ellie make it to the destination, but they recaive word a bomb is going to be dropped on their location. There is no time to escape, they both shed a few tears, and we see a shot of a bomb dropping, they both hold each other, we see the bomb closer to the ground, Joel says something to Ellie such as; "I'm sorry it has to end like this, but I'm glad we've met each other." Bomb is closer to the ground, Ellie says; "I've never met my real parents, (I'd assume she wouldn't) from what I remember, but I feel as though you're like my actually dad, Joel. I'll never forget you." Close-up of Joel's face as he holds back tears. Bomb is closer than before. Joel grabs Ellie by the shoulders and says; "Ellie, there's something I need to tell you, I- I should've told you this before" (I'd assume we'd discover earlier in the game Joel and Tess had a child during the quarentine that was taken away that Joel didn't know about until Tess mentions it and hints it could be Ellie. That child could be Ellie but it's not revealed) We see a far away view of the area Joel and Ellie went to, with a giant explosion coming from it and one of the military officers watching. The military officer then says "Targets killed, mission complete." The military officer would then pull off a mask of some sorts revealing him/herself to be one of Joel's trusted companions and the game ends.
I just hope that it isn't going to be the cliché ending of Joel dying to save Ellie. I mean we've seen it SO many times. For example the movies like The Road, The Book of Eli and Children of men (also the recent 1st season ending of the Walking Dead Telltale game) had that kind of ending. At least go the Babylon A.D route and kill the girl instead (that came out a little harsh, but you know what i mean). And yeah i know that they've (ND) said that Children of men was an inspiration, but i just hope that TLOU doesn't go the copy/paste route. And lastly i'm a HUGE ND (1st reason to buy PS4) fan and i love all their playstation games (not sure about the ones they did before PSONE), so i just hope that they're trying to do something atleast little different. I mean whats the point of making a new story that is the same that we've seen over and over again, there's no creativity in that. And i know it won't ruin the hole game but i must say that i would be a little disappointed (still huge respect for the company though) if thats how it ends. + I hope to see ND at E3 2013 with a new PS4 game.
TLoU will be secretly about In-N-Out Burger, the real reason that Joel was escorting Ellie to California was because he couldn't bear the though of a child having to live in a world without In-N-Out Burger.
At the very end of the game, they'll be pursued with the military and clickers and just when they're about to die they'll be rescued out of the blue by a bunch of people who pop out of portals with RoF M9s.
Specifically their rescuers will be Eric-ND, Jak, Daxter, Nathan Drake, Pogo, and Trumpet. Crash couldn't make the trip, BTW.
Then Joel and Ellie plus their rescuers will find the last intact and functioning In-N-Out Burger and they go inside where Joel orders a 4x4 done Animal Style with chopped peppers for himself and cheese fries with a Neapolitan shake for Ellie.
With a wink at the player, Joel says "Now that's quality you can taste!" and the game ends with the whole world blowing up before Joel can even take a bite from his cheesburger and Joel gets really **bleep** off even though he should be dead.
The camera then cuts to Master Chief and Super Mario holding a detonator with evil grins on their faces and we find out the sequel to TLoU will be about Joel teaming up with his Naughty Dog pals (except for Crash) to get revenge on Nintendo and Microsoft for ruining his cheeseburger.