Mark learns that his dad is an alien despot. He tries to fight his father, only to get beaten black and blue by his much stronger dad. While beating down his own son Omni-Man asks why he wants to save the Earth so badly when he'll end up outliving everyone he knows and asks what Mark would have left after 500 years. Mark, his body a mass of blood and bruises, responds:
Invincible: You, dad. I'd still have you.
Debbie's reaction to learning Nolan's true colors. She spirals into a deep depression, begins drinking, and at one point blames Mark for Nolan leaving.
Debbie: Why did you have to fight him, Mark? Why did you have to drive him away?
Rex Splode's funeral. Made NO easier by the conversation Atom Eve and Invincible have later. This, by the way, is AFTER Invincible has gone through a SERIOUSLY dark time in his life, including having evil doubles from all sorts of alternate universes slaughter thousands all over the world and fighting the absolutely insane Viltrumite named Conquest, a fight during which he WATCHED ATOM EVE GET KILLED. It's one of the best played "dark ages" in superhero stories, and it is done in just a few issues.
Mark and Eve's argument before he travels to an Alternate Universe to find Angstrom Levy, and him finally losing his cool and yelling at Eve.
Mark's rape by Anissa.
The whole Reboot? story arc, in which Mark is transported to the past and forced to relive the earliest days of his superhero career, and while things ultimately turn out a lot better than they did last time thanks to his knowledge of future events, the tradeoff is that his relationship with Eve and the daughter they had together no longer exist, a fact that he can't help but cry over every single night. Then when the entity responsible for his predicament appears and offers him the chance to stay in this new and "better" timeline permanently, he refuses and demands to be taken back home so he can be with his family again, knowingly sacrificing the countless lives his actions helped save this time around and dooming them to certain death. And when he finally gets back to the present, he discovers that five years have gone by in his absence, five years of Terra growing up without her father. What a gut-punch!
Ursaal hearing straight from the horse's mouth that Thragg doesn't care about her or any of his children; it utterly breaks her heart.
Anissa sacrificing herself to protect Eve and Nolan, and her last words are a sincere apology for what she did to Mark.
Nolan dying for real, and him telling Mark to lead the Viltrumites. Nolan's death is sad for what it is, but is for Mark: not only has he lost his father, but also the chance to live a quiet life with his family.
The Viltrumites can't stay on Earth...which means Mark has to leave. Even if, well...he made things BETTER.