- Near the end, where Scott's actually crying.
- Made more heart wrenching is when you take into account the actual build up of it. One, its Cyclops. Secondly, earlier in the film, Jean said she knew something bad was going to happen and Scott promised he would never let anything happen. When he tries to stop it from happening, Jean doesn't let him.
- Everyone's panic when they realize Jean's left the jet. Scott starts shouting, while Logan implores Nightcrawler to teleport out and get her, only to look horrified when he learns Jean is actively preventing assistance and rescue.
- The death of Lady Deathstrike. When Wolverine starts pumping her full of adamantium we're cheering—and then her eyes turn back to brown as she stares at him sadly, and we're reminded that she wasn't really a villain at all, she didn't deserve any of this. She's just a (probably) innocent woman who Stryker kidnapped, brainwashed and used to hurt people, and Wolverine clearly regrets having to kill her. There's a glimpse of her slowly coming to her senses earlier in the film and looking dazed before Stryker gives another dose of his controlling serum and back under his command.
- Watching all the mutants, then normal humans reaction to Xavier's burrowing into their brains. It's easy to guess most of them are just average people going about their day. Then for no reason other than prejudice (Stryker's and Magneto's), they're all racked with pain in their heads that they can't stop.
- The fact that hundreds of people, both mutant and non-mutant, probably died from it. People driving, people in delicate medical conditions, people who caught in the middle of something dangerous (like construction)... all dead. This includes children.
- When Stryker has Xavier captive, he reveals that Jason—who was once Xavier's student—resented his parents deeply, blaming them for his mutant condition. He tormented them with visions and illusions, until Stryker's wife "took a power drill to her left temple, in order to bore the images out." Stryker looks both contemptuous and on the verge of tears as he says "My boy. The great illusionist!"
- Jason's own situation within the film is tragic. His father had him lobotomized and used as a pawn in his scheme to kill all mutants, not even seeing him as human anymore. Despite this, it's implied a part of him still desperately seeks his father's approval. The last words of his mental avatar as it's expelled from Xavier's mind?
- Erik has tears in his eyes when he confesses to Charles that he told Stryker everything about his school and Cerebro whilst being under the influence of Jason's mind control serum. Even when he couldn't prevent it, it clearly hurts him that he had betrayed his friend, and endangered all of the school children.Magneto: I'm sorry Charles. I couldn't help it.
- There's also Charles' reaction when he sees the bruises on Erik's face. Even if they're not on the same side anymore, they still care about each other.
- Bobby's brother Ronny betrays him, Rogue, Logan, and John, and he doesn't show any remorse. Worse still, when he looks up while escaping into the X-Men's jet, his family is upstairs, looking at him in disapproval.
- When Kurt and Storm are discussing how baseline humans fear them and Kurt tells her that he pities them rather than hating them, Storm just looks at him evenly and says, "I gave up on pity a long time ago". She's one of the X-Men, the team whose motto has always been to protect those that hate and fear them, and she has to do it despite being hurt so badly by the world that she doesn't have pity left in her anymore.
Tearjerker / X2: X-Men United