Tristan's reunion with Yugi is pretty heartwarming. He gladly offers to join Yugi's forces, and Yami tells to him be at ease, noting it's nice to have a familiar face on his team.
Bakura makes a plan to help out by setting an enemy base on fire, but thinks he didn't do much to contribute. Yami Yugi tells him otherwise and is happy to have him on the team.
When Mai snaps Joey out of his brainwashing, she pretends to be offended when he can't remember what happened, but thinks to herself how relieved she is that he's okay.
Yami Yugi gets heartwarming moments with everyone in the game, and that includes Seto Kaiba. As soon as he hears Mokuba's been taken, he makes a plan to help get him back.
In Kaiba's campaign, he spares Bonz when Marthis is dead-set on executing him. This gains him Bonz's loyalty for the rest of the game.
Pegasus gives a very heartwarming speech to Kaiba about why he's in the resistance and hopes Kaiba will lead it.
Pegasus: I don't want the people of my land, or anywhere on this continent, to suffer anymore. The world could be a beautiful place: man and monster living in peace. But the trash needs to go first. I know that you have your own goals, but you cannot accomplish them on your own. You need help. You'll have that.
In Joey's campaign, after meeting up with Mai he promises to help her get out of the game no matter what happens.