I...I'm sorry. I...I just feel so far away from you guys...
- The intro of the game itself, with Heller having a phone call with his wife, Collete, and his daughter, Amaya, with his wife and daughter being in New York while he's on his military tour, looking forward to come home. The scene frequently cuts to news reports on the new outbreak of Blacklight in New York, and the reports that Blackwatch is in the city, while Heller is heard trying to comfort his worried wife, telling her to trust Blackwatch to deal with the outbreak. The scenes after the Title Card features news reports on the worsening condition of the outbreak, Blackwatch declaring martial law on NYZ, and that Alex Mercer is in the city. The final scene is Heller running to his home, and found his wife dead on the floor, with his daughter's doll is seen covered in blood.Amaya: I miss you, daddy!
Heller: I miss you too, baby girl. But don't worry. Daddy's coming home. - After his family's death, Heller is shown to be enlisting for a mission in the Red Zone, which is basically a Suicide Mission. His motive for doing so is either wanting revenge on Alex Mercer, or simply seeking death so he could reunite with his family.
- After encountering Mercer for the first time, and after he got manhandled by him, Heller took one look at the picture of his late wife, shown in the picture above, and decided to do a Self-Destructive Charge on Mercer, knowing well that it will kill him.
- The final conversation between Alex and his sister, Dana, after Heller absorbs him.Alex: This is no one's fault but your own—you do understand that.Dana: I understand that I had a brother once: a boy named Alex. A boy who used to play games with me, and go skating with me, and watch scary movies with me. I understand that... Alex is dead now.Alex: I am no longer bounded by "life" or "death", Dana. I've moved beyond that. Heller has as well. He just doesn't know it yet.
- The mere fact that Alex Mercer actually died. For anyone who's played the original Prototype and grew attached to him, this is really depressing. Alex doesn't even seem upset that he was defeated and actually laughs.
- Alex Jumping Off the Slippery Slope. Original Alex was a horrible person. Blacklight Alex finished the first game wanting to be a better person, and started Walking the Earth to try and achieve that. But instead he found so much betrayal and hatred he became completely fed up with humanity and became pretty much exactly what he hated so much in the first place.
- Father Guerra's death. Heller is just as devastated as the player.
- A remarkably subtle one from Blackwatch, of all places. While Heller is masquerading as a member of a patrol in a Red Zone, they chat amongst themselves, a standout being the following (paraphrased):Soldier 1: Hey, you ever wonder where you'd be without Blackwatch?Soldier 2: Dunno, man. Probably dead or in prison.Soldier 1: Yeah...me, too. *silence*
- It's in this exchange that Blackwatch stops looking universally like a bunch of Axe-Crazy psychopaths and actually becomes worthy of pity. The men that Blackwatch recruits are broken. Some of them don't care, others are blind to it, but the men in the patrol knew exactly why they joined Blackwatch. One way or another, they couldn't function in a world where the Blackwatch Creed didn't apply. And they know exactly where men like that end up when they try to live normal lives.
- Sometimes when you're in the Red Zone, you can find a civilian or two on top of the taller buildings. They're standing on the edge. They turn to look at you. Then they hold their arms out from their sides and just... fall backward without a word.
