For all of Chapter 3, Agnés has been pushing her friends away and generally acting like a jerk to them, to the point where even Tiz has to call her out on it. Then, on their way to the fire temple, the cavern breaks apart and Tiz and Egil are hanging over lava and Edea and Ringabel can't pull them up. Everyone, including Airy, is telling Agnés to go on ahead. Does she? No. She pulls a Crowning Moment Of Awesome, rescues Tiz and the apologizes to everyone for her behavior. It is at this point that the heroes become True Companions
After you defeat Barbarossa the Pirate, you can see his ghost haunting the Ghost Ship with the other dead crew... and he seems to be enjoying himself as always. Given that he was an extremely likableAnti-Villain, it's nice to see he's happy even in death.
In a late-game Party Chat, Agnés is revealed to no longer be a vegetarian. How did this happen? Apparently, sometime between Chapters 2 and 3, on the way to Eisenburg, the party ran out of supplies and was forced to spend their days fishing for food. One night, Tiz prepared a meal for Agnés only to have her refuse it. Ringabel has a little one-on-one with her both about Tiz preparing the meal for her, and about the fish sacrificing itself so she could live and she takes those words to heart. What makes this particularly heartwarming is that it this occurs while Anges is grieving over Olivia and hostile towards the party, and Ringabel is subconsciously remembering Braev telling him this long ago.
In Chapter 6, an event with Kamiizumi can occur, provided you've done a rather complex series of dialogue in Eternia in the preceding two chapters involving Mahzer, a gossipmonger in Gravemark Village, and Braev the Templar, in addition to awakening three of the crystals. Should you fail to complete these events, Kamiizumi is slain in battle much like in earlier chapters should you face him. But if you succeed, Edea instead has a heartfelt dialogue with Kamiizumi which is reciprocated and leads to a non-fatal sparring session.
When you first walk into the central healing tower, there is a little girl and a nurse next to her. Talking to the nurse reveals an anonymous man had, for the last year or so, been sending money to keep the little girl alive, and the nurse is very happy because the girl is now healthy and, with the money that had been given, was allowed to live in the hospital. If you look closely, her hairline brings to mind someone you've met... This is Ciggma Khint's daughter, whom you have unknowingly saved by killing off Jackal and Profiteur, allowing Khint to make money from the Kingdom of Anchiem by the King himself.
Holly and Barras slowly become closer over the course of the game. After one fight, you leave, but they just get up, as Holly quietly cast Reraise on them both during the battle. They're too weak to fight, but not too weak to spend the night together under the stars. Even better, Ringabel and the others noticed her casting Reraise, but they didn't finish them off because they were too adorable.
Whenever the Jobmasters team up
Barras and Heinkel backing up Ominas.
Jackal coming to Praline's aid.
Of course this means bad news for you.
(Though this also means bad news for you) Mephilia reveals in chapter 7 that with the combined efforts of Einheria's supportiveness and Barbarossa's strength/helpfulness, she was able to overcome her despair and obtain Susano-o.
Watching the Venus Sisters show that they care for each other dearly. In later Chapters, Artemia expresses her adoration of Einheria, and the scene where they all work together, even to challenge you, can be refreshingly heartwarming after the tragic ends they met in the first four chapters of the story.
In the later world loops, Braev increasingly becomes more forgiving to Edea, up to the point where he tells her that he's proud of her having grown up and finding a cause to fight for, which contrasts his attitude in earlier iterations where he refuses to see reason. Also, any interaction between Braev and Alternis. When Braev reveals that he's always considered Alternis his surrogate son, Alternis is shocked and deeply touched.
In Chapter Seven, Alternis will desire to train under Kamiizumi to get get stronger to protect Braev. The swordmaster will simply tell Alternis that he already has the strength of spirit and purpose to be as strong as he needs.
Durring Chapter 8's Boss Rush, the second group has Heinkel, Holly, Kamiizumi, and Kikyo revealing that they've worked together before 15 years ago. They spend the waiting time reminiscing...except Kikyo. She's then called out on it by Holly, and then reveals her nature. during her training, she would be made fun of because she spoke slowly. Kikyo found it easier to speak while in disguise. Cue Holly calling out the Swordmaster because it seems they didn't try to help her. Even though Kikyo tells her all of the Black Blades were patient and accepted her (minus one fat slug), it's nice to see that she cares. She even encourages her to speak normally when the heroes show up.
In the True Ending, every alternate version of your party fight back against Ouroboros' planet-eating magic, then deliver a simultaneous You Are Not Alone to your party, allowing you to defeat Ouroboros once and for all. Also overlaps with Crowning Moment Of Awesome.
Adding to that, it's not just the other versions of your party who's helping out. Across the various worlds, they are joined by DeRosso, Yulyana, Alternis, Commander Goodman, and more. Literally EVERYONE who is still alive across the near 10,000 worlds is fighting for you at this point.
While going to awaken the Fire Crystal, the party has to navigate an active volcano. If you talk to the Adventurer to save your game just before entering, he doesn't give his usual "It just gets worse from here on out..." message. What he says is, "Just try to be careful. That's all I ask." For a character whose messages are almost always neutral in tone, that moment of genuine concern really stands out.