From the very prologue of the first book, we have the death of Emily's dad. Even though he knows he's trapped and going to die, he tries to stay calm for his wife and daughter's sake and simply makes sure they're both out of the car before it goes over. Bonus for the part where Emily tries to pull the car back and can't, underlining how helpless she was in that situation.
Emily having to leave her mother behind to the arachnopod in the first book, especially since the shot of her letting go of her hand mirrors that of her mother letting go of her father's hand. For a moment, the implication is that she won't ever see her mother again.
Then when she actually does rescue her mother, she's already in a coma from the poison and Emily is convinced that it's all her fault for not rescuing her sooner.
The Stonekeeper's Curse
Considering Trellis was a villain in the previous book, him getting punched by the guards is pretty much Laser-Guided Karma. But then you read his past later on in the series, you can't help but feel sick as you go back to this part.
Karen is still comatose, and when Theodore left after bringing breakfast, Emily can't help but break a little bit. It's clear that even after several days, she still blames herself.
The Cloud Searchers
Luger's breakdown. It's hard to tell that the emaciated, timid elf is the same person as the boisterous, ruthless commander of the King. He took a really hard fall (both literally and figuratively).
Trellis's situation. It's bleak enough that his father and people are mistreating him, but it'll be even worse now that his chance to live is gone when he failed to kill Emily. Now, he's being hunted down, likely killed if he wasn't imprisoned, and is on the run because of it, with an unlikely chance he'll ever return home due to the soldiers and bounty hunters on his trail and he doesn't have any allies or resources on enemy territory and he still has to worry about Luger. He's completely on his own, and at the end of his rope. It's sheer luck and basic decency that Emily and co. came along and helped.
The Last Council
The Reveal at the end of the fourth volume. Ronin and Pierce were dead all along, and Max was just using them to continue his facade in front of Emily. Emily looking back and seeing their stony faces was just cruel, especially since she didn't know what it meant at first even though the audience had already seen this curse in action.
The Prince of the Elves
He only has one friend Layra, who was an elf and her parents were imprisoned because they were elves. Just how many more families were unjustly persecuted because of their race?
His father is emotionally cold and pressuring. He doesn't eve give him the freedom to choose his own future.
It borders on Nightmare Fuel, but after sending them off to the safety of Gulfen and one last hug from Laura, they were immediately killed by the Cielis Guard and Max, overcome with emotion, retaliates, killing four soldiers.
The fact that Max got 50 years just for liberating an innocent family and will fave further trial in Korthan for killing the soldiers.
It gives you a pang of pain when Max looks at his dad but he doesn't bother to reciprocate or even give words of comfort. Instead, he avoided him with disgust. Max, without Laura and her family, is very much alone.
Worst of all, he manages to escape Korthan later, but is severely injured and on the brink of death. His life is a miserable mess and it's going to end in a tragedy. And even when he accepted the Voice's deal, it doesn't really go for the better.
It's minor, but Trellis mistook Emily's scolding for concern prompting her to insensitively explain the concern wasn't for him, but for the people affected by their actions. Even after all he's done, she doesn't really consider him as a friend yet.
It's minor, but the implication is quite sad. Luger tries to discourage Trellis from entering the Void and to listen to what the others have said, but Trellis laments on why he should listen to them when they won't listen to him. It kinda hurts especially to people who just wanted to be heard but is instead cut off or ignored.
Trellis's memory. Easily one of the most emotional parts of the series. Trellis enters to Void in hopes of changing the course of history, avoiding the war, but instead he got something worse: the full weight of what he really lost.
Consider this from Virgil's perspective. He may be only a memory, but he is experiencing current Trellis in the past. One day, a person just dropped out of the sky, his face scarred, clearly neglected and doesn't recognize you? That's your nephew, whom you are currently caring for and loved. By the time he sends him off, it's clear he knows that Trellis suffered but has no choice but to accept and let them happen for the greater good.
[Virgil and Trellis enter an open balcony.] Trellis: What's going to happen to you, Virgil? Virgil:[he doesn't face him] Best not to worry about me. Whatever happens is suppose to happen to lead you here. Virgil:[looks at him] Just promise me you will remember all of this. Remember that you come from a good family. And the shortcomings of my generation must not extend unto yours. Make us proud, Trellis.
Trellis's Hidden Depths. You wouldn't have thought he was insecure, which would likely stem from harsh treatment from both his father and his people, who have in multiple times in the series express their incredibly low opinion of him.
Trellis: You know I'm not a good stonekeeper, Emily.
Emily being genuinely upset over her Stone lying to her about how much influence he had over Max. Even though she says she never fully trusted him, you can see through the other volumes how she had treated him as a confidant when she needed him.
Emily, Trellis, and Vigo manage to land unscathed thanks to Trellis Max was not so lucky. He isn't dead, but severely injured with several broken bones and likely internal bleeding. The Voice forces him to move, to which he admits he can't, prompting the spirit to mend his body (and it isn't pleasant). He just begs him to stop but then the Voice brought up an old wound:
The Voice: What would Layra say if she saw you now? Max: [delirious with pain] Layra.. I'm so... Sorry, Layra. Max: Please... Forgive me...
Escape from Lucien
The Reveal behind Trellis's uncharacteristic cruel impression in Book 1: he was possessed by a Dark Scout all along. They way he justs asks Max what the creature was when back then he tried to sic it on Emily, tells you that there is somethingverywrong. How long was he brainwashed? How many people became his victims while he was possessed? The expression on his face is just awful.
It becomes Harsher in Hindsight when Max revealed that no one, aside from Emily, has ever succeeded liberating anyone from a Dark Scout's control, and that no one actuallysurvived when they do. It means that when the Elf King sicced the parasite unto Trellis, he was condemning him to die.
Max's death from rapid aging in the Void. Despite all he had done, Emily was still upset over it and tried in vain to keep him from dying.
And immediately before that, Max's conversation with a memory of Layra and her parents.
Layra: We never asked this of you. Please, stop.
Max: Layra, I wish you were here to see what I've done. I made them pay. I made them suffer for what they did to you and your family.
In the seventh volume, Emily begins having dreams about spending time with her father—on a camping trip that he died before they could make. The first one is especially sad as he insists everything is alright and she bitterly replies that's not true.
What makes this worse is that she is talking to the Voice. She knows that she is not speaking to her real father but she keeps doing it anyway... which really shows how much she misses him. And how desperately she wants to have him back.
Trellis in the seventh book also has to suffer through seeing his own childhood, and predictably gets to watch how abusive his father was to him. And what makes this worse? He was just silent as his life was changed terribly in the span of a few minutes. He doesn't get outraged or yell or even try to intervene with the memory, he just left because he had enough. Trellis may not have said anything, but it's obvious that he's hurt and affected by the memory and Emily could see it.
Then, afterwards, he sees Emily transform into a fire monster out of rage and is utterly unable to help, which hits him especially hard because Emily was able to save him from Sybrian and Luger from the Stone. He can't return the favor. Trellis briefly pleading with Emily to show him how to save her and then commiserating on his failure later is tragic to watch.
Trellis investigates the memory cube given to him by Gabilan. And quickly enough, he encounters a cramped house in the middle of a tundra. Inside, he sees an unconscious elven mother and child, frozen and starving. It's quickly revealed that the boy is himself, and the mother is his own. When Trellis was a child, his last moments with his mother were of them starving and cold, holding each other in bed to have what little comfort they have. He woke up to her corpse. And the clincher? Young Trellis wasn't even crying, or wailing. He was just quiet as he processes his trauma. Not too different from current Trellis's reaction in the Nexus when he sees his father scar him. The extent of his trauma goes so far back and it's horrifying.
Trellis'sface. It's one of the few moments he actually showed such devastating emotion. He wasn't even angry, yet instead just seems tired from it all. He just wished he had a memory of his mother.
Trellis once again has a bout of Heroic Self-Deprecation during the celebration dinner after they captured a contingent of elf soldiers, wherein he insists he's not a hero despite all he's already done to help the war effort. He sure feels awful guilty not helping the people of Ippo enough.