The Last of Us: to make a right choice

The hardest puzzle in this beautiful and touching story is the words Joel said Ellie at the very end. There are at least two ways to treat them: this may be the truth or this may be a lie. But this may be the truth and a lie at the same time. Let's see, how this can be. [spoilers]

Joel, Ellie and the rest of Humanity fight famous Cordyceps, a mutated variety of the fungus which is able to subjugate not only insects but also humans. Ellie had been bitten by an infected person but managed to stay alive for two weeks after that, while an ordinary human turns into a zombie in two days. She is completely immune, and she is of interest to Fireflies, a group of militant rebels who fight FEDRA (the federal power which controls several quarantine zones inhabited by non-infected people) and in the search of the cure. Ellie says that they in search of the vaccine, and she may be the only key for it.
Although, at the end Joel swears that there were dozens people like Ellie, and Fireflies are not search for the vaccine anymore, so she should not sacrifice her life. It's possible to understand him, Ellie also saved his life (from ordinary infection) by administering penicillin, and he can not lose a daughter for the second time, because Elle has became as a daughter to him. Can anyone do something different after that scene with giraffes? He may have lied Ellie to make the loss of her friends to look not so futile. But did he actually lied and had doomed humanity to perdition in exchange for his personal happiness? We may find the answer at Marlene's and surgeon's recordings.

Marlene recording 1
It's five thirty pm on April 28th. I just finished speaking... heh... more like yelling at our head surgeon. Apparently there's no way to extricate the parasite without eliminating the host. Fancy way of saying we've got to kill the fucking kid. And now they're asking for me go ahead. The tests just keep getting harder and harder, don't they? I'm so tired... I'm exhausted... and I just want this to end... So be it...

Marlene recording 2
Hey Anna. It's been awhile since we spoke. I um... I just gave the OK to precede with the surgery. I really doubt I had much of a choice. Asking you is more of a formality. I need you to know that I've kept my promise all these years. Despite everything that I'm in charge of, I looked after her. I would have done anything for her and at times… Here's a chance to save us. All of us. This is what we were after. What you were after. They asked me to kill the smuggler. I'm not about to kill the one man in this facility who understands the weight of this choice. Maybe he can forgive me. Oh, I miss you Anna. You're daughter will be with you soon.

Surgeon's recording

April 28th. Marlene was right. The girl's infection is like nothing I've ever seen. The cause of her immunity is uncertain. As we've seen in all past cases, the antigenic titers of the patient's Cordyceps remain high in both the serum and the cerebrospinal fluid. Blood cultures taken from the patient rapidly grow Cordyceps in fungal-media in the lab... however white blood cell lines, including percentages and absolute-counts, are completely normal. There is no elevation of pro-inflammatory cytokines, and an MRI of the brain shows no evidence of fungal-growth in the limbic regions, which would normally accompany the prodrome of aggression in infected patients. We must find a way to replicate this state under laboratory conditions. We're about to hit a milestone in human history equal to the discovery of penicillin. After years of wandering in circles we're about to come home, make a difference, and bring the human race back in control of its own destiny. All of our sacrifices and the hundreds of men and women who've bled for this cause, or worse, will not be in vain.

Basically, this means that there may be other partially immune people (the surgeon talks about her case, and there were other MRI images at the university and the hospital), her immune system is able to hunt Cordyceps (high antigenic titers), but there is no immune reaction (white blood cell lines are normal, and there is no inflammation). This means that something in her body makes the fungus inactive (there is no evidence of fungal growth in Ellie's body, but the fungus grows in fungal media). The surgeon probably wants to get the cell culture of her brain to play with in the lab. So, Fireflies not search for the vaccine anymore (a vaccine is needed to train the immune system), but hope to find a cure which is equivalent to penicillin (which is able to destroy Cordyceps). There are guys at discussion boards who argue that penicillin is the fucking fungus, and this means that Joel has lied. But the surgeon talks about the equivalent medicine (nothing suggests that it should be fungal), and it's clear now, that it should suppress the Cordyceps. Most likely, Fireflies tested the vaccine on apes at the university, but failed with it, since the apes were infected. So, Joel actually had told only truth, and this was his very subtle lie.

The presence of other cases of immunity (probably with immune response) suggests that there is a parasite-host coevolution, and Humanity is not doomed actually: Ellie's children may be the actual Humanity's hope. Ellie may bear a mutation which is able to suppress Cordyceps without the immune response.

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