- At the end of your last mission to Olympus Coliseum, Phil ends up saying "Roxas, don't be a stranger", showing that he started to care about the Nobody.
- The interactions between Roxas and his friends are a prominent moment. It's what contributes to the massive Tear Jerker ending.
- A minor one, but seeing Organization XIII from the perspective of someone whom they aren't opposing, as largely Punch Clock Villains, is kind of nice.
- This particular scene, made even more heartbreaking because you actually see Roxas's and Axel's friendship in this game:
Roxas: (as he's leaving the Organization) No one would miss me.
Axel: That's not true! [more quietly] I would.
- Meta example: The game is dedicated to Wayne Allwine, late voice actor for Mickey Mouse.
- Roxas taking Xion up to the clocktower for ice cream.
- Maybe it was minor, but it was really nice seeing Riku interact with Xion and Namine, throughout the game. He would always try to make sure Roxas, Xion, and Sora could all live on, independently first, before even making an attempt to revive Sora at the cost of the others. That was always his first question when DiZ or Namine told him he'd have to interfere. What's more, he didn't force Xion to rejoin with Sora, either. He took the poor girl under his wing, explained the situation to her, and looked out for her. Riku let Xion make her own decision. He didn't fight Roxas until the very end and he only intervened because Xemnas would have turned Roxas into a Dusk or just killed him; not only because it would keep Sora from waking up, but because he promised Xion he'd protect Roxas. Riku was never really as bad as he thought/said he was.
- In the manga, during the time period when Xion had trouble summoning her keyblade, Roxas suggests that if worst comes to worst, he and Xion should run away from the organization together, and that if they do they should invite Axel to come with them. When Xion manages to summon her keyblade again, she's elated, but also expresses that she liked the idea of running away with Roxas and Axel. Later when they are celebrating Xion's keyblade returning, they ask Axel if he'd be willing to live with them after the organization completes its objectives. Axel accepts their offer and thinks to himself, with a smile, that they make him feel like he has a heart. While in the game Roxas also eventually suggests that the three of them run away from the organization, the manga version happens much earlier in the timeline and shows just how much on all sides that the three of them want nothing more than to be together.
- Xion's Cuteness Proximity with Pluto in the manga. In a meta-sense and in-universe-sense, it's strangely nice to see two characters of differing art styles and origins bond so well together (even if Pluto's been bugged by DiZ to spy on the Organization) and seeing Xion gush over a Big, Friendly Dog.
- The best part? Saix allowed Xion to keep Pluto. When Axel lampshaded his decision, Saix merely responded that it's because it reminded him of his fondness of dogs in the past.
- The first person to give you a present just from talking to them in The Grey Area before a mission is Larxene. Which is kinda nice, even if she does tell you to take a hike as she gives it to you.
- She and Marluxia, on their last day in the Grey Area, both regret being unable to induct Roxas into the fold of their conspiracy. Again, kinda nice, all things considered.
- Also, even though his interactions with Marluxia, Larxene, Vexen, Lexaeus and Zexion weren't always positive, Roxas is genuinely distressed when he learns that they've been eliminated and that he won't ever see them again, and also disturbed at how none of the other Organization members seem to care about their deaths like he does.
- In the manga, Roxas' face upon seeing Axel (whom he thought to be "annihilated" in Castle Oblivion) is unbelievably cute!
- Another moment in the manga is when Riku stops Roxas from attacking him in public, not wanting innocent people to get caught up in their conflict over capturing an imposter or looking for a dangerous renegade girl.
- Also in the manga, Roxas and Axel travel to different worlds to look for Xion. They're aided by Genie and Carpet in Agrabah, and Hercules and Phil in Olympus Coliseum, which shows how much these characters grew to view them as friends, and willingly help them out.
- The Neverland chapters of the manga end up having the weirdest heartwarming theme to them - that being how much Peter Pan and Captain Hook mutually care about each other as enemies who give each other's lives meaning.
- A number of the secret reports, particularly those written by Xion and Axel, have heartwarming (sometimes crossing into Tear Jerker) content and give insight to their own views of friendship. Highlights include Axel proclaiming that finding out Xion was a replica didn't invalidate the friendship he formed with her, showing that his suggestion to go to beach with her and Roxas was so they could forget their troubles. And Xion spelling out that she loves Roxas and Axel, even knowing that she probably won't be around much longer.