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.
An odd example on page 7. While around ninety percent of the page just looks like a technical diagram for an SC 50, the clear implication of the exploded diagram is that this image is a tasteful way of depicting Mort's death.
Mort expressing his desire to be taken to the ether, and how he seems to have long ago accepted the idea of this.
Mort: I want to help you! And… I've had enough. You guys have been really great friends… But, you're getting older, and I never will. I think it's time for me to move on.
Kat fighting back tears as they prepare to send off Mort.
Annie leads Mort to the afterlife, and she kisses him goodbye. He blushes and says "Thank you...miss." He's already forgotten about Annie and Kat and the rest of his friends.
Bonus page 47, The Stinger. Pro patria mori, Silenti, Dulce et decorum est. "To die for your country, be silent, it is sweet and fitting." After everything we learn about Mort the phrase just becomes all the more heartwrenching. Somehow, with just a few panels of props and hallways, Gunnerkrigg Court feels more haunted despite the fact it has one less ghost.
Possibly worse if you recognize the reference to Wilfred Owen's "Dulce et Decorum Est," a poem that condemns World War I. The entire point of the poem is that if more people witnessed the horrors of war, they "would not tell with such high zest / To children ardent for some desperate glory, / The old Lie: Dulce et decorum est / Pro patria mori."