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In the same part, after hearing throughout the story the same line about how "the unnecessary people will die, and all others will live forever", the shopkeep simply stating that "there isn't a single person who is unnecessary" is just...
Elle breaking down and crying at the beginning of the game because she fears that she would not see Ark again. She's completely right.
The moment when Ark learns he couldn't talk to animals anymore, when Leim rescues you and when you realize, after basically creating this whole world and developing the towns (and buying Ark an apartment), you have to leave it.