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.
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: