- The sad fate of Ben, a fellow glader. It wasn't his fault he got stung by a greiver, but he still had to be banished by the rules of the Glade. Even worse in the film version where, amidst his infectious sounds, he's pleading to be kept in the Glade.
- Chuck's death. He gets in the way between Thomas and Gally and takes a knife for his trouble. To think that he is the youngest Glader...
- Then you find out that WICKED had implanted control chips on every Glader, casting doubt whether Chuck's sacrifice was voluntary or not. Still, it is a tragedy anyway you look at it.
- Not to mention Gally. No matter how much of a jackass he is to Thomas and the others, he is very clearly forced to do what he did. The third book confirms this. Gally was forced, and he now has to spend the rest of his life haunted by the memory of stabbing his best friend.
- During his introduction, Aris recounts that he experienced the same situation as Thomas did at the end of Phase One, in which a brainwashed Glader is forced to kill another. But this time, there is no counterpart of Chuck: Aris had to watch his telepathic best friend and Thomas' counterpart, Rachel, die by stabbing. Made even more poignant when you learn that this is one of the few things Aris didn't lie about during the time he is with Group A. Aris and Rachel had been friends since they were children, just like Thomas and Teresa. And like Teresa, Aris does not undergo Swiping, so he knows Rachel a lot more than she did about him.
- Teresa's Heroic Sacrifice. Partly because it's so sudden (it happens in the third book's penultimate chapter) and yet also redemptive to the character's story arc.
- The slow sinking of Teresa's and Thomas' relationship in the books. Going from them being close friends and partners pre-brainwipe to Thomas distrusting Teresa more and more and not even considering her a possible ally later on is just plain sad. And the worst part is that Teresa knew he would stop trusting her and deliberately started down this path to save his life. She chose the option to give up Thomas so he could live rather than resist WICKED and let him die as her friend. Paired with her physical Heroic Sacrifice later on, Teresa is the character that gave up everything for the person they loved. She gave up on WICKED in the same way, if not more, than Thomas, and his failure to realise that this girl sacrificed everything for him to live when it is so blatantly obvious is just heartbreaking.
- Teresa does not like to indulge in the past, or the causes of problems in general. Anyone who has read The Kill Order will know why. She has lost her family, friends, and finally, four strangers who risked their lives so she could contribute to the betterment of humanity. In summary, she has experienced unspeakable horrors long before she becomes involved with WICKED.
- Speaking of The Kill Order, prepare for the waterworks while you are reading it. Just when you think it couldn't bring out more nihilism, it does.
- The initial release of the Flare virus and the death of the Three Stooges: Darnell dies painfully and slowly; Misty chooses to remain behind; and Toad is mercy killed by Alec.
- Mark's flashbacks to the Flare radiation event. Especially the bit when Baxter is killed.
- Halfway through the book, Mark realizes that everyone: him, Trina, Alec, and Lana are infected. He gives up trying to save himself and dedicates his remaining time to send Deedee to Alaska.
- Alec mercy killing Lana.
- Trina, in her Flare delirium, loses her memories of Mark.
- Mark, Trina, and Alec's Heroic Sacrifice. One word.
- Every single scene with Newt in the third book, particularly his last chapter and ESPECIALLY page 250.Newt: KILL ME! Please, Tommy. Please.
- And then, in The Fever Code, we get to see his famous suicide attempt. The way it describes his resignation and despair is just heartbreaking, and then when he jumps and it doesn't work he's in so much physical and emotional pain that you just want to hug him and make all his problems go away.
- The epilogue of The Kill Order, which tells the time when WICKED yanked Thomas away from his mother. They exchanged very brief goodbyes and the latter valiantly fought back her tears; she didn't want her son away, not after the loss of her husband to the Flare, but her other option was to let him see her slowly turning into a Crank. Once Thomas and WICKED left, she immediately burst into tears.
- Every time Sonya is mentioned in the original trilogy becomes Harsher in Hindsight once you find out in The Fever Code that she is Newt's younger sister. Newt's greatest wish - that the two live together again - never comes true: for around the next eight years, the two spend time apart due to being assigned different barracks, but at least they still manage some contacts. Once the tests start, Newt and Sonya are irrevocably separated, both by literal walls and because they are Swiped; when they meet again in the Scorch, none recognizes each other. After the tests end, Sonya allows her memories to be restored, but Newt doesn't. We all know what happens to Newt after that. The only silver lining of their tragic tale is that Sonya survives to the very end.
Tearjerker / The Maze Runner