The Last of Us Part II can't be fully understood without reference to the first game, which ended with Joel making a fateful choice. While Ellie began as a just a traveling companion he needed to protect (because she's the only person in the world who's immune to the Infection), by the end she's become his surrogate daughter in all but name. When it turns out that making the vaccine requires Ellie's death, he chooses to keep her safe. He personally kills a number of Fireflies, and he implicitly kills many thousands or millions of people who would have benefited from the vaccine in the long run.
The game ends with Ellie expressing doubt about Joel's story and emphasizing the importance of the vaccine. If a vaccine had been available from the beginning, it could have saved millions of people, including people who Ellie knew and cared for personally. Likewise if a vaccine could be made available now, it would prevent untold tragedy in the future. Joel lies to her, swearing that he did nothing to prevent the Fireflies from making a vaccine.
I think that the intended conclusion was that Joel made the wrong choice. Yes, we love Ellie just as much as he does. Yes, we understand why he did what he did. But even so, Ellie is not more important than millions of innocent people put together.
This leads to an interesting quote from the Creative Director: "What's interesting to me about the ending is, I think people who aren't parents are about 50/50 in how they feel about the ending, as far as agreeing with Joel or disagreeing with Joel. I haven't heard a single parent say 'I disagree with Joel's decision.' " [1]
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It appears that more than half of all players missed the intended message of the ending. (Granted, Druckmann doesn't come out and say that, but it seems an obvious conclusion based on the plot.) In that light, it appears that the entire second game is dedicated to hammering in that original point. Joel did make the wrong choice. Joel loved Ellie deeply, and that's admirable, but he had the fatal flaw of exclusively loving the people he knows personally while giving little thought to offscreen strangers. The entire point of Part II is that strangers are no less important than the people you know personally, and any moral system that fails to take strangers into account is bound to produce bad outcomes in the end.
Did you love Ellie because of her deep connection to her (adoptive) father? Well guess what, Abby had just as much connection to her father. Did you think that Ellie was precious because of that wonderful moment she had with the giraffes? Well guess what, Abby had an equally wonderful moment with a pregnant zebra. Did you scream for vengeance when Abby killed Joel near the beginning of Part II? Guess what, that's how Abby felt when you killed her dad at the end of Part I!
The importance of the vaccine is repeatedly emphasized. We see graffiti from someone who brands the Fireflies as "liars" because they failed to provide a vaccine (or just save the world in general, but obviously a vaccine would have done that). We see two dead lovers, one shot and the other transformed into an Infected, who were once heroic people who risked their own lives to help others. A vaccine could have saved them both. And of course the entire game is full of Infected, any one of which might have been saved by Ellie's vaccine (depending on when they first got infected).
The game explores how deep love can actually lead to terrible deeds if it's shortsighted. In the beginning we're led to assume that Ellie doesn't know why anyone would kill Joel; from her perspective it appears to be a random act of cruelty. Later we find out that Ellie had already forced Joel into a confession. She knew what he had done to the Fireflies, and she knew that logically he deserved to die too. Her love for Joel leads her not only to mourn his passing (which is understandable) but also to go on a Roaring Rampage of Revenge against the people who killed him, even though his death was largely justified!
Her revenge quest is filled to the brim with concrete examples of why this is a bad idea. She brutally tortures one of Abby's friends for information. (This friend was a nurse and generally a good person). Her human enemies all have names, and the death of a random mook is often met with "No! Ethan!" or the like. She abandons Tommy in his time of need just to go after Abby. She ends up killing a pregnant woman, and she's horrified when she realizes what she's done.
All of that just builds up to the second half of the game, where you play as Abby and see things from her perspective. The Wolves are humanized even further in this section, and Abby herself learns a lesson in caring for "the enemy" (Seraphites, in her case), eventually turning against her own leader to protect Lev.
The player finally confronts Ellie from Abby's perspective, being forced (once again) to see what Ellie's actions look like from the outside. Abby actually shows Ellie mercy, allowing her to live even though Ellie has already killed most of Abby's friends by this point. But Ellie still can't let it go, and eventually she tracks Abby down again.
Ellie by this point is so conflicted that she ends up rescuing Abby just so she can kill her. When Abby refuses to fight, Ellie threatens to kill Lev just to motivate Abby. It's an insane situation, and it's portrayed that way. Ellie, motivated by the strength of (adoptive) family bonds, is now threatening to kill an innocent person in another (adoptive) family, just because another member of that family (Abby) wanted revenge for the death of a member of her family (her dad) who was killed because a member of Ellie's family (Joel) wanted to protect his adoptive daughter. But if everyone had originally considered themselves members of a single family ("The Family of All Mankind", if you will), then we wouldn't be in this situation. If Joel had allowed Ellie to die, we would have a vaccine and the world would be a much better place. And if Abby had allowed her father's death go unavenged, or if Ellie had just allowed Joel's death to go unavenged, many smaller tragedies would have been avoided.
Ellie nearly kills Abby, but backs off at the last moment. Her thirst for revenge has finally been quenched, and she finally understands the insanity of what she's done. Abby and Lev go free, and Ellie goes home. But she still pays a price for her misdeeds. For one thing, she appears to lose Dina, her girlfriend. Her devotion to a dead person has harmed her relationship with a living person. She also lost two fingers in the fight, so she can't properly play the guitar anymore. Playing guitar is something she learned from Joel, and it represents her truest self. In other words, her connection with Joel has led her to partially destroy that very same connection with Joel. Narrow-focus love doesn't just destroy others; it destroys you too.
Speaking of guitar, Joel plays a song for Ellie at the beginning, with the lyrics "If I ever were to lose you, I'd surely lose myself." On first glance it's a beautiful expression of fatherly love, but on reflection it's something more. It's literally saying "I would go insane if I lost you; I don't know how to deal with the grief of losing you." Joel "lost" himself when Ellie's life was in danger; he did terrible things to keep her safe. Likewise Ellie "lost" herself when Joel died; she did terrible things to get revenge, and ending up losing major parts of her own life (Dina, playing guitar, etc.). Once again we see more of the downsides of narrow-focus love.
At the very end, we see a flashback where Ellie tells Joel outright that he should have let her die. She knew, intellectually, that he made the wrong choice. But her emotions got the better of her, just as his emotions got the better of him. The game isn't saying that love is a bad thing, but it is saying that you can't just love the people you know; you also have to love strangers, at least to some degree.
In the end, Abby is actually the more justified character. She killed a man not just for personal reasons but also because he had deliberately chosen to doom millions of strangers to Infection. (Though granted she still could have just left him alone.) She stood up for Lev even though she could have easily dismissed him as an "enemy". She had the chance to kill Tommy and Ellie at the beginning but she decided to be merciful. She was merciful again when Ellie tracked her down in Seattle, which actually led to her getting saved by Ellie later on. Ellie, meanwhile, knew all along what Joel had done but decided to avenge him anyway.
In the end we still care about Ellie. We understand why she sought revenge. But empathy is not approval. You can care about someone while still realizing that they did wrong. This is how Ellie related to Joel after she learned the truth. But she didn't take that lesson completely to heart. She couldn't let go of the need for revenge. And that's why she suffers.
And if Joel had made a different choice, none of this would have happened at all.
