Albert's speech about the graves in the town plaza, and his utter moral outrage at the people trying to film the FAYZ at the end.
Caine's letters. Especially the second one. And Diana's reaction to it; "She read it again and again. Each time crying. Each time laughing." It's a little too much to handle.
Sam and Astrid inviting Diana to live with them. After all she's been through, it looks like Diana has finally made some genuine, real, healthy relationships which aren't bore out of manipulation. Seeing just how much she has grown since book 1 is heartbreaking and beautiful.
Poor, poor Dekka Talent. She lost the woman she loved and her parents still don't accept her.
The most painful moment of the book for Dekka (and possibly in general) is her reaction to Brianna's death. She's cradling Brianna's body and crying into Edilio's shoulder, and Edilio, who also believes the person he loves to be dead, has no choice but to force her to suppress her emotions so that she can keep up the fight against Gaia.
The revelation that both Caine and Sam were in fact, legitimate, despite Connie's suspicions.
Sam: But that means Caine lived his entire life without... Astrid: Without love. Sam: But not in the end. In the end he found it.
Just this effing line; "Turn out the light Sam."
And also; " You are now free to leave the FAYZ."
Hunter in PLAGUE. Actually, Hunter all the time.
A running motif in the series is Sam mentally putting himself on trial and wondering what he would say to the adults if the FAYZ ever came down. How could he explain why their children are battered, starving, and traumatized, or why the town is burned down and in ruins, or why there's a large graveyard in the plaza?
Brianna's death. One of the most cheerful people within the Fayz, tried to save everybody only to end up getting axed by Gaia.
Computer Jack's death. Even before the Fayz he was getting pushed around into situations he didn't want to be in. He never wanted his powers or have to fight against Gaia and was perhaps the most cowardly person in the Fayz. In spite of all that he makes a heroic sacrifice helping Sam escape only to be gunned down in the crossfire.
Duck Zhang's death. He was arguably as cowardly as Jack as he hid in his closet reading comics while everyone else was fighting the Coyotes during Caine's assault. On top of all that he gets bullied by Zil who also turns of the normals against him when they find out he's a mutant. In the end it was only thanks to him sacrificing himself that the Gaiaphage was weakened for a while. He spends his last few moments sadly relishing in the fact that he finally did get to be a superhero as he plummets deep into the Earth.
Dahra's death. Ever since the start of the Fayz she tried her best to nurse the sick and wounded despite not having healing powers like Lana. In spite of all her good work, he narrowly escapes getting eaten by Coyotes only to then meet her doom when Gaia destroys the boat she was on.
Mary Terrafino's death. She made so many selfless sacrifices on her behalf, taking care of the little kids despite having so many health conditions herself and what was her reward? She gets tricked by Nerezza into almost killing them all, ends up deformed and injured outside the dome and spends her last moments lamenting on how she couldn't save the kids.
Roscoe's death. He gets infected by the greenies and Edilio is forced to lock him up against his wishes meaning he has no choice but expect his slow and painful end.
E.Z.'s death. Within seconds of his introduction he meets his end as a Red Shirt. And Sam is forced to burn the remains.
Cigar's death. After being torched by Penny and turned into a Cloud Cuckoo Lander he brutally gets mauled by the Zekes.