Uhhhhhh...... Question???? Spoilers????

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I just... finished playing through the Sakura event story.... and, let's just say the ending caught me off guard, like, left field-terminal velocity kind of surprised. Not to give out too much info on this cuz there is not much to go on about anyway as far as I am aware. But to address the elephant in the room: What is with the whole "Commander is a terrorist now, plaster its face all over the TV!" thing? Did I miss something? I thought we were still traveling towards Lviv??