TearJerkers are for post-viewing analysis and contain unmarked spoilers.
- Shortly after 9's awakening as he explores the destroyed world around him, he comes across the deceased bodies of a mother with her child in her arms. Even though he had only been awake for a short time, he's still understandably disturbed.
- In hindsight, the Fabrication Machines backstory is tragic. It was created by the Scientist using purely his intellect as an instrument of human progress. After that, the Scientist noticed that his creation was flawed and dangerous because of its lack of human soul, but before he could give it one, the Chancellor took it away from him, so he could use it to mass produce war machines. Without a soul to withstand corruption and being forced to make armies of robots beyond its limits, it finally snapped and reprogrammed its machines to kill off every lifeform as punishment for its tormented fate. Word of God even described it as an abused child who finally got the power to fight back.
- 2's funeral, what happens right before the end (sad) and the end (happy?). The music makes it worse.
- 1's last words. He may have acted like a Jerkass for most of the history, but his declaration that "They left us nothing. Nothing. Why do we have to right their wrongs?" really puts in scope that he's VERY bitter with being abandoned in a dead planet with machines hunting them down because of the Chancellor's greed. Try to imagine this: You're left with only a few others like yourself, after surviving a war caused by a single human's misdeeds, in a completely destroyed and dead planet with horrifying creatures that want to kill you for your souls, and you alone are left with the task of protecting them, while being the size of a toy. In a way, 1 is a Shell-Shocked Veteran who's been pushed way over the Cynical side of the scale.
- In a weird way, the Machine's reaction to the death of the Winged Beast. The Winged Beast's head is brought to the Machine and the latter just gently cradles the last remains of its dead creation in its hands. For a moment, it almost looks mournful...and then, it crushes the Winged Beast's head and tosses it aside, furious at having been foiled.
- 5's death, because just when he finally gets some self-confidence and takes a level in badass, he gets killed desperately warning his friends and pleading for his life.
- 6's death: seeing him just fall limply into the mist...
- The Seamstress has been scared off and 1 isn't that enthusiastic about letting 9 save the dolls she's kidnapped after what happened last time, motioning over to 2's body, which 5 is sitting with, straightening it out and touching it.
- The ending, where 9 says goodbye to the souls of 1, 2, 5, 6, and 8, especially when it shows 5 looking at the survivors at first not wanting to go but 9 reassures him.