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Well what exactly do you expect her reaction to be other than stunned?
You have to consider the situation surrounding the radio noise back then when she doesn't know anything, compared to now when she is more aware... Enough to have noticed Awaki trying to do something that might restart the experiment.
Then you have to consider what is the scene that is unfolding in front of her.
And lastly, Mikoto was not the same girl she was before when she found out about the project.
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