- Bradley's comments before Victor kills him:
Bradley: I always thought it would be Wade who'd come knocking on my door.
Victor: Wade's dead, Bradley.
Bradley: I'm not afraid, Victor. I'm not afraid of dying.
- Wolverine forgiving Kayla after discovering the reason that she's working for Stryker; he's been holding her sister hostage. And her death. And Logan finding her body, eyes open after bleeding to death; he doesn't recognise her, but still closes her eyes to give her more dignity.
- Victor coming back to save Logan from Weapon XI, telling him "Nobody kills you but me."
- Logan coldly severs his ties to his brother after their battle with Weapon XI, but Victor proves his love for him once and for all:
Logan: This changes nothing: We are done.
Victor: No, we're not. We are brothers; and brothers look out for each other. [runs into the sunset]
- It's a small moment, but during that Uncomfortable Elevator Moment with Team X, Dukes chuckled (along with Bradley who more openly giggled) in amusement while observing Wade Wilson's Motor Mouth behaviour. It may not be much, but it shows that while there are violent members in the team like Victor and Agent Zero or those who are Only in It for the Money like Wade, there are also genuinely decent-hearted guys among them (Bradley and Wraith are also pretty good guys). Furthermore, it also shows how much the film gives Adaptational Heroism for Dukes, considering that he's a villain the comics.
- Logan's interactions with the elderly couple. They see a completely random stranger run into their barn, naked no less. And what do they do? They clothe him, they feed him, and they give him a motorcycle. It makes their deaths pretty tragic, especially considering what Logan just went through.