This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Angel's Egg
The scene when the man and the little girl are talking in the girl's "house" and he says something along the lines of "maybe we aren't real, maybe we're all just a memory of someone else, and it's raining outside".
It's easier to name the parts that aren't soul-crushingly sad... The dead, empty world where everything and everyone has forgotten their purpose, the little girl's death after the man she just got attached to shatters her egg/symbol of hope, when she dies just before she can reach him, the grim, alternate Noah's Ark story where the olive leaf never came, and last but not least, the half-sunken Ark itself amidst the black, endless sea...
Chris Stuckmann on Youtube has a more positive explanation of the ending: the little girl's faith held true despite being questioned by the man, so when he destroyed her egg, he was releasing her from her test. She died, but in doing so her faith was rewarded a hundred-fold, giving birth to many more eggs that would grow into the birds she believed was in the original egg all along. She is memorialized among the spaceship's statues as a testament to her unquestioning faith. Which, while still grim considering the surrounding world and the implication of what happened to humanity, at least implies a sort of hope for change.