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Tear Jerker: Gunnerkrigg Court
From Chapter 6: A Handful Of Dirt
Given how Annie usually acts, seeing her break down emotionally like this is very upsetting. In this case, it's important that that's where her emotions (all of them) started flooding back, period. That's bound to go a little differently.
The idea that Annie had to be the Guide for her mother is highly sniffle-worthy. Kat's reaction on the next page helps somewhat. The fact that Tom Siddell didn't add a little snippet of wit at the bottom and instead just left it blank lends to how sad that page really is.
Skywatcher's monologue at the end of that chapter:
"I continue to turn my face upwards, measuring the same temperature, the same humidity, radiation and thousands of other variables. But now a new metric has been added. The number of angels I have seen is "one". And I will keep watch for more."
The Bookends around the most directly depressing section do a good job of showing how context is the difference between Narm and Tearjerker.
There's something very quietlyheartbreaking about Ysengrin's body, and the way it has withered away from the proud wolf he once was. And more than that, Ysengrin seems to be deeply resentful of his own physical weakness without the suit of bark armor he wears. To see such a proud figure filled with such self-loathing is, in its own way, quite painful. In Coyote's own words, he seems so... pathetic despite his anger, pride and hate.
Kat "deactivating" the robot at his requestat the end.
Then there's the next page after that...
Robot: Let it be known. In this tomb of ancients, the angel called forth a spirit of the dead. You see how easily she gave life, and how easily she took it away.
From Chapter 35: Parley and Smitty Are In This One
Shadow 2 was kicked out of the forest by his own family for not hating the people of the court.
Robot, as he's laying damaged in Kat's workshop, unaware if Shadow is going to be okay or not
Robot: Why didn't I realise it before? I love my good friend, Shadow.
From Chapter 37: Microsat 5
It starts right from the beginning, with Annie's reaction to being called by her father. Then, it gets worse when she learns that he was just using a code, with Annie's name as part of the code - in other words, he wasn't even calling her.
From Chapter 39: The Great Secret
While Annie was living in the forest, she formed what seems to be a pretty strong friendship with Ysengrin. Which makes it pretty heartbreaking that he's willing to do this as soon as he even suspects she might think of him as inferior to humans.