* The end of the first chapter: the Hatter's frenetic and pathetic attempt to have another tea party with his now deceased friends (who were trying to kill him just a second ago) is extremely sad and disturbing at the same time.
** The Hatter's death. After all the trouble Alice went through to help him, after a short but awesome moment in which they work together, and after a CurbStompBattle that can only be described as a CMOA. Made more poignant by the fact that the Hatter died having (or trying to have) one final tea party with his dead comrades.
** Made worse when Alice's response is essentially [[WhatTheHellHero "Eh, screw him, he deserved to die. ... Oh, guess I'm drowning in tea now."]]
* The Carpenter's HeroicSacrifice where he pushes Alice out of the path of the Infernal Train, revealing his evil ways were actually an attempt to protect the Deluded Depths from the train. His cry of "The death of a dream!" is just harrowing.
* The scenes on the Infernal Train where all of Alice's friends call her out for her ignorance.
** The Mad Hatter berates Alice for letting Dr. Bumby manipulate her mind to turn her into an empty husk.
** Caterpillar calls Alice out for noticing the child abuse around her but being too focused on her own troubles to speak out about it.
** The Queen of Hearts reveals Lizzie's [[RapeAsDrama cruel fate]]. Alice has a HeroicBSOD.
*** To make it worse, Alice sounds like she's on the verge of tears the whole time she's with the Queen. And the Queen is Wonderland's version of her sister.
--->'''Alice''': My Lizzie! ...Oh no, p-poor Lizzie...