- Human relations with mutants have improved considerably. The government has Beast in a high position, and found a way to reverse mutations, but made it purely voluntary or for use in self defense. It's also implied but never outright stated that many of the people at the picket line against the cure were normal humans chanting that their mutant friends don't need any so-called cure.
- When a newly resurrected Jean tells Scott to open his eyes for her he initially resists for fear of killing her. When she assures him she can quell his powers, he trusts her and opens them. Giving him the chance enjoy normal sight for probably the first time in years. Shame it all went to hell for both of them seconds later.
- Throughout the series, the films show the great respect between Charles and Erik even when their respective factions are at war with each other. When a Brotherhood member (in this case, Pyro) tries to talk disparagingly about Professor X, Erik will have none of it:"Charles Xavier did more for mutants than you will ever know. My single greatest regret is that he had to die for our dream to live."
- He also looked genuinely horrified as Jean killed Xavier. He screams "Charles!" as Phoenix kills Xavier; it's clear that he still cares deeply for Xavier.
- Mystique taking the cure dart meant for Magneto.
- Watching the X-Men come to the aid of the soldiers defending Alcatraz. When Wolverine starts dishing out orders for them to stay safely back, you'll notice the men appear more than happy to cooperate.
- Leech is a sweet kid who seems to hold no ill will toward the people who either want to use him, or even those trying to kill him (though he still seemed pretty terrified of Juggernaut).
- In addition, despite being used primarily as a resource for the cure, he appears to be very well taken care of at Alcatraz Island, as there are plenty of toys and a games console in his room and Dr. Rao seems quite gentle and motherly towards him.
- Beast's meeting with Leech is very sweet and a little sad. Hank introduces himself and reaches to shake the boy's hand ... only to see it turn back into a human hand when he gets close enough to Jimmy. Jimmy initially assumes Hank is upset and apologizes before Hank reassures him it's fine. It's especially moving when you keep in mind that Beast looks the way he does due a failed attempt to cure his own mutant side, and using Jimmy's power is the closest anyone has come to making that possible.
- Warren saving his father. Despite all the pain that exists between them, there's still something of a healthy relationship there.
- Wolverine telling Rogue only to go for the cure if it's what she wants, not what "some boy" does. Though he insists he's not her father, that was some very paternal advice coming from him.
- Kitty is very gentle with Leech, saying she's here to rescue him. When he negates her powers to phase through the walls, he apologizes, explaining he negates mutant abilities. Nevertheless, Kitty protects him from the Juggernaut who fortunately has his powers negated as well. They then go the old-fashioned way, through the doors and corridors as well as the holes that Juggernaut made. He survives to the end of the movie, becoming a new student.
- In a deleted scene, when Bobby, Piotr, and Kitty try to convince the adult X-Men to let them help, Kitty says that being an X-Man means protecting those that hate and fear mutants. Bobby points out that they're a family.
- Magneto, in spite of hating humans throughout the series, does show that he does have some grounds for sympathy, as he spared the family that was in the vehicle when he moved the bridge. Its unknown if that is because of them might be mutants unknowingly, but at least Magneto has a heart not to just kill the humans in spite of his racist genocidal views towards them.
Heartwarming / X-Men: The Last Stand