I have a new theory on why Joel lied to Ellie at the end. There are several scenes early on in the game. When Joel and Ellie begin traveling with each other alone. After Tess, had died.
To understand the logic of this possible theory you, have to look at the earlier scenes.
1. After the Capital Building scene when we find out that Tess, is infected and decides to "sacrifice herself" for Joel and Ellie in those last moment. We can tell that this does bother Joel a lot about her decision to do this.Even though he knew she, was going to die from the infection. After both Joel and Ellie enter the hallway beyond the double doors. This is the first time in Ellie's mind that she lost someone apart from Riley's death.
By the time they exit the subway tunnel and Ellie, tries to bring up Tess's death to Joel...he remarks " You don't ever bring up Tess...ever! In fact lets keep our histories to ourselves." in this way he is saying this to Ellie, that he, really loved Tess...but could never say the words to her. And that Ellie, has no right to invade his private memories and feelings.
This can be looked at as the first time that Ellie steals from Joel...because the way she internalizes the death of Tess as someone that she loved. Instead of seeing that it was Joel, who lost someone. This display of disregard for his feelings. Shows Ellie's own selfishness.
Then she repeats this again with the death's of both Sam, and Henry before they reach the hyrdoelectric dam scene. Ellie internalizes their deaths as loved ones. When in fact both Sam and Henry were people that she hardly knew. Even though in the end scene with Sam dying and Henry committing suicide...Ellie never brings them, up at that moment.
2. Now lets discuss the Hydroelectric Scene and Ranch Scene briefly. This is when Maria, tells Ellie about Joel's dead daughter. And Ellie,steals the picture, of Joel and Sarah even though Joel, has no idea that she took it. This can be seen as a desecration to Sarah's memory...and Joel's feelings about the death of his daughter.
This is another moment of Ellie stealing from Joel all over again.
Then there is the Ranch Scene with the heated arguement where Joel says to Ellie " You are treading on some mighty thin ice here."
Then Ellie replies back " I am sorry about your daughter Joel. But I have lost people too."
Then Joel says " You have no idea what loss is!"
Ellie replies back with " Everyone I ever cared for,has either died or left me...Everyone except for you!"
This just another form of Ellie's display of selfishness and disregard for Joel's feelings.Plus later on she sews him up after he is impaled at the Uninversity.Without asking him if he wanted to die to finally be at peace.Which is no different when Joel makes Ellie's decision for her at the end in the hospital. And kills Marlene, which in turn robs Ellie of things from her.
Even though later on he acts like he is not bothered by it when Ellie admits she stole it. And hands it back to him.But in fact more than likely is bothered by the fact that she took it. And just puts up a front that he is not just by saying " I guess you, can't escape your past. Thank You." .
The point is Ellie robbed from Joel in different ways. As much as Joel robbed from Ellie at the end.
That is why he lies to Ellie about the truth of what happend in Utah at the hospital. He figured he was going to get something out of this hell that he was put through in that one year. Being saddled with a child who was (disrespectful, selfish,etc.).
So in the end Joel had every right to lie to her about everything. And rob her of the cure and of Marlene even if it meant him "sacrificing a relationship" with Ellie where she did not care about him in the first place. And Ellie has no right to blame him for robbing her of those things.
Because lets be honest they were right back at the end of the story not liking each other. Just like how they were in the beginning. Neither one could trust the other anymore with the truth.
Final thoughts is that Ellie by the end needed to learn what true loss is. With the death of Marlene, and being robbed of being part of a vaccine. This was something she needed to learn through Joel, since she had no experience of what true loss was other than Riley's death. Which her friend's death was not her fault.
And Joel, in 20 years has lost more than both Ellie and Marlene could ever loss put together.
A persons personal loss will always out weigh the lost...of material lost and desires of things.
In Joel's case for him what he lost on the personal level.
On Ellie and Marlene's case it was what they lost on a material level...that is until Joel turned it into a personal loss for Ellie by the end. With robbing her of both her choice and killing Marlene at the same time.
Was Joel justified in doing all this? The answer is "Yes he was." .
Just like from Ellie's point of view she more than likely feels that she did nothing wrong towards Joel. Both characters can be seen justifying their own actions and decisions. From their own view point at every turn in the game.
But again like I stated before. This is just another possible theory on the ending of the game.
Like everyone else that is a fan of TLOU ...I am a fan of both Joel and Ellie.
Also just like everyone who would like to see them come back in a sequel. So would I. This way both character can have a chance to work out their differences between each other. And come to some kind of understanding of what happened.
And hopefully be able to rebuild that trust between each other again...as well as their love.