Sad thing is, medically, there was no reason to require Ellie's death. In fact, the best scientists, even ones that are psychpathic mad scientists, would recognize that Ellie being alive in the hospital for a long stay with lots of tests over the years is worth more than a hack job of a surgery to cut out infected parts of her brain.
You literally do not need to get an entire sample of the cordyceps parasite directly from the brain. You just get a sample from her blood or other bodily fluid, it's the exact same thing. Then there's this thing called "culturing" where you take a basic strain of something and just grow more for lab use, not a big deal.
Also, the immunity is within Ellie, or likely the interactions.
I would have loved to see it end instead on a note where you have a crazy scientist who wants all the credit for saving humanity there and then, trying to grab as much samples directly to speed up the process. Then, a more reasonable scientist trying to get Joel to help.
In the end, they could still need to have a risky surgery. One where they don't know if it will be successful, and Ellie makes the choice to go through with it. Ellie and Joel have a really heartbreaking talk before the surgery. Then as she's being prepped and laid down on the table, you flash back to Joel laying Sara down, coming to grips with his loss, and now potential loss of Ellie.
I cringed the moment I heard Marlene say some BS about needing to kill Ellie. If they'd gone with my route, we could also have skipped that terrible section where you're dodging soldiers.
In the end, knowing the science and medicine behind it could have led to a more interesting outcome. Not only that, if they wanted to leave more room for a sequel, it's easy enough to say, as others have pointed out, that a vaccine would take a long time to develop, and even if there was one it would take a long time to distribute.
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