The penultimate chapter, 64, is possibly the saddest chapter in the whole manga. We see a shot of all of the children that have died so far, walking in a line against a white background, chatting and laughing with one another. The scene goes over several double pages, and right at the back we see Ushiro running to catch up at the rear, with his sister Kana, his friend Kanji and Machi, the girl who loved him, turning and smiling as he arrives. They continue to walk out of sight, and the next double page is completely blank. They were gone. They'd moved on.
It's hard to pinpoint a sure heartwarming moment in such a sad series, but Daiichi's chapter sure is a peak. He's so compelled in being the nicest person as possible to everyone around him, especially his brother and sisters after his father ran away from home that it's just depressing to see him try his best to hurt as few people as possible and not damage the theme park he was going to take his siblings to on that same day the battle occurred. His fight ends in awesome, but the chapter itself ends in even more tears as he chooses not to have his corpse brought back to his family, so they'd think he just "disappeared".
And if you follow the anime, there's a sort-of epilogue: Kana, the Sole Survivor of the game, is starting middle school and living her life as much as she can after Ushiro and the other kids's deaths. Then she finds an embittered young boy killing some little insects in frustration and sadness because his brother left him, mirroring Kodama's actions in the first episode... Yes, he's Santa, Daiichi's little brother. Futaba (his sister) tries to explain what happened, but the Kana stops her, and start telling them what truly went on with Daiichi. *sob*
In the manga, it's worse. That father of theirs? The one that supposedly abandoned them? He was helping a friend who ran into some trouble and returned home shortly after Daichi's fight. Daichi never got to know the truth.
And then there's Maki's fight... Not only we see the kids forced to watch the destruction of the universe the defeated pilot comes from, but then we have Maki breaking down... then she manages to see her baby brother's birth through Zearth and even gets to briefly hold the baby in her arms, before she passes away almost in peace.SNIFF.
No mention of Chizu's backstory (or heck, her story full stop) in the manga? It's especially distressing to see her pounding on the door of the hotel room she's been locked in and screaming at Hatagai-sensei to let her out, just after he's revealed his true colours and set her up to be gang raped by his friends. Then there's her final words just after her battle, where she regrets that the baby she's carrying, which is doomed to die along with her, couldn't have been born to her older sister instead.
In the manga, after killing Kako, she briefly reflects on how the pilots are growing used to their members dying, which is a fairly depressing thought considering that her turn just came up and she's going to die at the end of the battle. Worse, still, while she had been willing to forgo taking revenge against Hatagai or committing suicide for the sake of her baby, now she realizes that her baby will die as well, and she has nothing left but revenge against those who raped her.
"I learned to talk like you... by watching you on the TV..." Oh, Anko, you poor baby...
Speaking of Anko, her fight in the manga brings out further tears of an almost uplifting kind. As footage from inside Zearth is broadcast of her bravely fighting on even after both her legs have been burned off by acid, the public comes to see her as a heroine. She may never have gotten to be an idol like she'd wanted, but in a way, she's gotten to be something even better. *sob*
And then there's Komo's pre-death "World of Cardboard" Speech in the manga, in which she plays the piano as a part of the trap for the other pilot, thinking about how she has come to notice the world around her... and after the Batman Gambit works, she smiles and falls dead on the floor while her father calls out to her. Made even worse when Admiral Komoda quietly asks if he's even worthy of holding his daughter's body in his arms, and his assistant tells him that he is, because Komo passed away happily.
For repeat viewers, the first battle qualifies, as Kokopelli looks up at all those empty chairs...
What about the scene where Kana tells Jun "I want to die too!"?
The "Kana's coffin was so small" bit.
Especially sad, if you've watched the anime first where she survives. And then there's the previous scenes where various characters tell Jun to take care of Kana. *sniff*
The part where Machi and Jun visit the other pilots' families. Especially the part where they go to Nakama's mom, and they tell her that they gave each other nicknames to get to better know each other. The sheer look on her face when she hears that they nicknamed her Nakama... GAAAHHHHHHHH.
Special note should be given to the Honda family, who are essentially working to atone for the collateral damage Chizu did in hunting down the people who raped her, and Chizu's father doesn't believe that he can force Hatagai to take responsibility for his actions after what Chizu did. It's quite sad to see their reaction to not only what was done to Chizu, but also what she did herself.
Chizu's father: "My daughter being both a tragic victim and as a cruel murderer are two sides of my daughter I must accept. Therefore, no matter how much my daughter was victimized, as her father, I must take responsibility for the other side as well."