The raid on the Red Flag meeting in the Season finale, everything after the order is given to the tactical team to return fire. The soldiers take it as an order to "fire at will," shooting everything they take to be a threat. The Alphas they're facing are often very dangerous people, but then they start shooting Alphas who are already lying on the ground or just trying to flee, and the gas they tried to use to subdue everyone makes it hard to tell actual threats from terrified noncombatants from their own allies, so they just shoot everything that isn't them. And for every Red Flag member you see fighting back with lethal force, you hear screams in the background of people calling out for their friends and loved ones who are probably being gunned down. The scene in which Rosen stops a soldier from shooting Gary, telling him that "he's one of us," is juxtaposed with one of other Alphas being shot in the back as they try to flee.
Gary finding Anna dead in the Season 1 finale, after he had run into the midst of a raid, ignoring the danger and eventually harm to himself because he was afraid for her. Made about fifty times worse by him not realizing at first that she's dead and telling her that it's okay, come on, he'll help carry her. And then he just keeps saying her name and begging her to come with him. And then a soldier pulls him away from her and tries to arrest him, and Gary starts beating on him with his own nightstick and screaming "No!" over and over, nearly getting himself shot before Rosen intervenes. And even then Gary just goes back to calling for Anna and trying to pull her to him, even though she's clearly dead.
In season 2 it's revealed Gary has begun screaming in agony every morning because of the trauma Anna's death caused. As part of his daily routine, no less.
Nina's backstory in season 2. Finding your father bled out on the floor would be bad enough, but Nina knows it's her fault even though she only wanted her father to stay.
The part where John tells Rachel that he's sorry about her friend (Nina), and Rachel says "I wouldn't really call her my friend anymore." Considering how close she and Rachel used to be, (remember Nina teaching Rachel to walk in heels?) this just goes to show how different things have become in the space of a few episodes. Thankfully, they do make up.
Rosen having to turn in his own daughter for being The Mole. Made so much worse by how relieved she is. The scene in custody, with her begging him to send her to building seven, rivals Gary's discovery of Anna's body in season 1. That Dani is so worn down by being caught in the middle of this conflict that to be reduced to an automaton and sent to live out her days in prison is the best outcome she can think of...
And then her Heroic Sacrifice, counting on Parish caring enough about her to not detonate the bomb...and then he does, while her father and lover watch, powerless to help her. Even Parish wishes he hadn't done it, but it's too late.
Heh. Powerless. 'Cause it was an electrical explosion. Heh heh.
The scene in "A God's Eye View" where Gary is standing in the middle of Grand Central Station with the dead bodies of thousands of innocent people. The moment when he's just staring at Rosen's dead body is just... heartbreaking!
And that's where the series ends, since it was canceled. Damn!