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Tear Jerker: C Control
Kimimaro's teacher losing his wife and children after being defeated by Yoga.
After losing to Kimimaro, Sennouza Ko implies that the children he had saved may have either died because Ko never managed to help them.
Mikuni's backstory. Let's just say it involves a sick little sister and we'll leave it at that.
When Jennifer Sato ended up being bankrupt by her deal with Mikuni. While she was sliced in half and bleeding out black bills, she passed on her Asset, Georges, to Kimimaro. Even though we know that she's alive, she looked like she was dying and now has no future.
The ending. Kimimaro's in a world where he shouldn't exist...
And before that, Mikuni opting to stay behind in the world of "today" (the one which had lost its future), plus Q and Msyu disappearing along with the FD. It gets sadder when Kimimaro pulls out a photo of himself with Mikuni, Q and Msyu at the end, considering that their chances of meeting again may well be zero.
And even before that, the dreamlike sequence where Mikuni talks to Takako, only to realize he's become a lot like his father, who stopped Takako's transfer to another hospital for financial reasons. And then he sees that she's gone. You can hear that he's on the verge of tears.