- Shouko's Heroic Sacrifice. Especially since it immediately segues into the end credits, which close on an image of other Fafner pilots crying, and the singer going (in translation): "Please God, give me just a little more time".
- This is made all the worse in the Light Novel, where the reader isn't even SHOWN the sacrifice, and is only treated to the visit to the grave.
- Kazuki admitting that all he ever wanted was to apologize to Soushi for taking his eye out. When he is made to choose to either live or disappear he doesn't really pick one; all he basically says is "I want to really talk to him one last time," which saves him. The way he crumples over the console at the thought that his most important person hates him is utterly heartbreaking.
- The scene where Kouyou bids his friends one last farewell before turning into a Master Festum to defend the island.
- Sakura being assimilated, while being mind raped and losing herself all alone and struggling desperately to remember Kenji.
- After Soushi is trapped by an incredibly strong Festum and starts to exhibit signs of disorientation, Kazuki begins to shed tears of distress, shaking Shoushi's 'prison cocoon' and crying his name. This soon evolves into all-out rage and desperation when the Festum kidnaps Soushi. Kazuki propels himself high into Earth's atmosphere in pursuit, screaming:
Kazuki: GIVE HIM BACK! GIVE ME BACK SOUSHI!
- Mamoru's death. It happens quickly compared to Shouko's death and Kouyou's assimilation, but somehow that makes it more powerful, especially his vision of Sakura and Kenji holding hands right before he dies.
- Soushi disappearing at the end of the season, and Kazuki's reaction to it. It's the end of a Trauma Conga Line that leads him into being a Broken Bird in Heaven and Earth.
Right of Left
- Just saying "pretty much the whole special" should suffice, but special mention must go to the deaths of main characters, Ryo and Yumi.
"Good Boy. You went straight to your master's side, didn't you?"
- The graffti: "Everyone will be gone anyway". A few words that says a lot.
- The worst part? They all ended up disappearing anyway
- Just when we thought that with the end of Heaven & Earth Kazuki might catch a break, Exodus reveals that he only has about three years left to live before the assimilation phenomenon takes his life. Not to mention that Soushi is desperate to save him, and actually chose his career path in hopes of finding a cure.
- Chizuru and Fumihiko telling the parents of the third generation pilots that their kids will be going into battle. The expressions of absolute anguish and despair are heartbreaking.
- There's a room/shrine dedicated to the people who have lost their lives in the war against the Festum. The walls are covered with pictures, and among them we see Ryo, Yumi, Shouko, Michio, and Mamoru.
- Although it appears at first as though he's accepted it, Kazuki doesn't want to die. This is something he hasn't told anyone, and one can only imagine how long he's kept this bottled up.
- The thing he wrote on his wish talisman before crumpling it up and saying he hadn't decided yet? "I want to live."
- Canon begging Kazuki not to leave and breaking down when he does.
- When Yumiko gets crushed by the collapsing building, Miwa attempts to climb up to reach her, even though all that's left is a hand protruding from underneath the rubble. Then you realize that she's literally a 4 year old in an adolescent body and probably doesn't realize that her mom is dead.
- Akira attempts to save a bus full of innocent civilians from a Festum attack. Despite the fact that he gets there in time, everyone gets assimilated anyways and he's left holding what's left of their bloody clothing and a few assimilation crystals. This kicks him into a Heroic BSOD, followed by Broken Tears and a Roaring Rampage of Revenge. Watching and listening to him have a breakdown, especially over the comm as Hiroto is subjected to, is awful.