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Tear Jerker: Revolution
"Home": Emma trying to convince Bass to let everybody go, and Bass realizes she isn't trying to manipulate him. Even so, he says he is no longer the Bass she once knew.
Bass: You see the best in everyone.
(A few moments later)
Bass: Lock everyone in the basement. Burn it all down.
Maggie's death is sad itself, but with later plot development it was revealed that Georgia has intercontinental trade relations. If she survived ten more episodes, she would likely be half-way to her family by now.
The flashback to Bass's "family dinner". He may be the villain, but seeing him sobbing that he has nothing left while he has a gun to his head at the graves of his parents and sisters is gut-wrenching.
The death of Jeremy Baker, who was actually a loyal Only Friend to Monroe despite his psychotic tendencies.
Randall Flynn's backstory with his beloved son dying at war.
Nora dying in Miles's arms.
Atlanta and Philadelphia were hit by the nukes. Especially hard-hitting is that it means Aaron couldn't kill the power in time. And Rachel blames herself, as well.
Danny's death. He finally graduated from The Load and took down an enemy helicopter with a rocket launcher...only to be shot by said helicopter as it crashed. Danny may have been a Base Breaker, but even people who weren't sad to see him go were hit hard by the shocked and devastated reactions of the others.
The end of "Everyone Says I Love You": Miles passes out from an infection and it's not made clear if he's alive or not. Then, Horn catches Aaron and Cynthia and demands that Aaron fix his brain tumor. Despite Aaron's desperate pleas that he can possibly do something if he just had some time, Horn fatally shoots Cynthia, and Aaron, who had earlier spoken to a boy who was a projection by the nanites, asks him to "Kill 'em All", which he does. Afterwards, the boy/nanotech asks why he asked him to kill Horn and his men instead of save Cynthia; Aaron then asks him to, but he refuses, confused by Aaron's temperament, and disappears. The episode ends with Aaron desperately begging him to come back.
Dreamcatcher: When Aaron starts to really realize that the world he's in, with the power back on, isn't actually real. Man, poor guy. And to think the dream-avatar of Charlie Matheson was who had to give him the bad news.
Austin City Limits: Charlie has to kill Jason. She does not take it very well.
When Neville is having his BSOD, Charlie matter-of-factly tells Neville he should kill her. It's only at the very last minute that she wants out, and she counts the gun being empty as a second chance for her.