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Zawarudo I had said something back in Batoto about similar complaints.
One thing is sure here, it's not speculation, the "government"(I say this, but it's probably just one organization, the government itself may not be endorsing their actions after all) are the bad guys here.
Nana herself has just started noticing how inconsistent her mission is.
It doesn't matter how smart a scientist is. Thos "Expected Casualty" numbers are clearly bullshit. If anything they always show similar numbers, which is curious because these kids have powers that doesn't suit those numbers even if they banded together to rebel against the government.
They would probably count on that "their powers may evolve" bullshit to explain those exagerated numbers.
But even then, how would they even begin to predict what kind of evolution would their powers go through?
Nana is a brainwashed assassin hired by an organization, fed bullshit in order to kill people who have dangerous powers, disregarding whether they are bad kids or not.
2 of Nana's victims were clearly good guys, she murdered them in cold blood under the assumption that they might become a threat in the future.
Those bullshit numbers are there to give a sense of urgency and keep Nana under control, you know it's that one theory in which "the danger is so big that even 1% is a big risk", I don't remember the name of this theory but one other author used a similar thing in a recent manga or anime. I remember someone even posted the theory itself, which I remembered and added in my on theory for Talentless Nana.
In my view Nana is an expendable, whether she is successful or not, the organization clearly wants everyone on the island dead including Nana herself.
One other point, not a single narrator in this series is trustworthy. The author is clearly hiding something here, I've read bad "survival" stories many times, but this one still shows promise, even after all the bad twists. (Mostly because not a single time did the author actually convey that Nana is in the right. I swear, read it again, there is not a single time in which the author tries to convince us that Nana is the real hero, much on the contrary, he stays "silent" even after so many deaths. Even the past event in which power users caused a catastrophe is only told by a newspaper and who even offered that info to Nana? Yes someone, the same ones who has given her those missions, we can't even verify the truth about the situation, as the power users may have been defending themselves instead, after escaping from an institute or something). I'll still keep my words, it's too soon to judge this one as bad.