"Welcome back, big bro! I wanted to see you so much!" Admit it, seeing Nanako again made you all warm and fuzzy inside. And afterwards, Yu having dinner with Nanako and Dojima and his inner monologue mentioning how much he loves them, that's just icing on the d'aww cake.
During Aigis' ending, her conversation with Labrys in the limo after she finally realizes that the indirect reason she met P3's main character at that pier was because she had unconsciously inherited Labrys's sincere wish that her successors could meet someone they loved and truly be happy. When Aigis thanks Labrys for this, telling her that her wish had come true, and Labrys begins to cry, some people can start to tear up right along with her.
Aigis constantly refers to Labrys as her sister. When Labrys decides to work with the Shadow Operatives to catch the mastermind, Aigis practically jumps with joy at the prospect of working with her big sis.
In the stories of Yosuke, Chie and Yukiko, they get confronted by their Shadows (actually the Malevolent Entity), who proceed to rip their resolve a new one, telling them that they want the P-1 Grand Prix to happen because they want to feel needed or avoid boredom again. They're on the verge of falling to despair and reject their Persona again, until Rise gets the rest of the team or whoever's available to support the character that this time, they got friends to support them even during bad times in question, bringing resolve back to them and kick their Shadows' asses again.
The sequence where Labrys accepts her Shadow and befriends the main cast, in pretty much any of the story routes.
Teddie's route, after the fight with Naoto. He was really torn up by her illusory words, so making up after the fight was satisfyingly sweet.
What's more: Teddie glomps Naoto after winning and, surprised and everything, she hugs him back!.
In Elizabeth's route, you learn that Makoto's Heroic Sacrifice in the third Persona game was not a complete sacrifice. He's not dead, but in a deep slumber, and Elizabeth now works towards awakening him.
Also at the end of her route, after Curbstomping Yu in a fight, the rest of the Investigation Team shows up and threatens to fight Elizabeth for hurting him. Shows how much of True Companions they really are.
At the start of Yosuke's story, he decides not to call Yu up & tell him about the return of the Midnight Channel because he didn't want to panic his best friend by telling him the Midnight Channel was back whilst he was out of town & unable to help.
When Yu is forced to fight a wicked-speaking Yukiko, she summons her Persona, which Yu observes. He knows she is not herself, thinking "the real Yukiko should have a beautiful heart like this."
In Akihiko's ending, he tells Mitsuru that he's going to leave the Shadow Operatives eventually, as he can't stand by and let small crimes go unpunished while he's working towards a larger goal, as he is now. Mitsuru's reaction effectively boils down to "That's it?", showing that she knows Akihiko well enough that she'd already figured that out. She goes on to say that they'd be able to work something out so that Akihiko work for both the police and the Kirijo Group, and that he shouldn't underestimate his value to the group.
In Yukiko's story, she and Labrys stop by a classroom to get some character development. Labrys start talking about her looks, and Yukiko decides to help her. When she's done with the make up and whatever Yukiko brought with her to the TV World, Labrys can only mutter "I never thought I could be this pretty...". Given the Broken Bird aspect of Labrys's character, this little moment is one of the sweetest Yukiko has with another character in the whole game. Made even better when Yukiko goes to Junes to buy fashion stuff for when Labrys comes back.
Remember the Bittersweet Ending of Persona 4, where Yu has to leave his friends? Yeah, like THAT was gonna last. That final line from Yu's story mode is sure to brighten the day of any player of Persona 4: their story isn't over just yet.
Yu: The Investigation Team is back in action!
Yu referring to Yosuke as "Partner." Whilst this is Yosuke's nickname for Yu in the original game, it's good to see that Yu does the same to Yosuke - he actually does consider Yosuke his partner, very fitting for the two who started the Investigation Team in the first place.
It was a really small thing, but at the end of Teddie's route when Labrys is leaving, Teddie starts to get upset, and Yosuke, without prompting, starts to scratch his head in a form of comfort. It's small, but when you think about it it's actually really sweet.
There's also Chie's adorable admiration of Akihiko.
When encountering Teddie and comparing him to the General, Mitsuru and Aigis think he is "adorable" and "charming", respectively.
In the manga adaptation, which focuses on Yosuke, he goes over to comfort Labrys when she is dealing on how she felt no one would understand how she felt. How does he do so? He shares with her about what happened to Saki, his own feelings of sadness and frustration on the tragedy and how he was able to overcome it with his friends. It's a powerful show of empathy given how much it still is raw for him and how he is becoming more willing to open to people. No wonder he's Yu's partner.
Rise and Aegis' reactions to Yosuke pouring his soul is also this. Rise's saddened face reflects her loving and feeling nature. She did not know Saki, but that doesn't matter. It's a tragedy she died and she can feel how much Yosuke still hurts from her loss. Aegis meanwhile is flatout horrified. She's heartbroken to hear of how this innocent person died in such a callous manner. Furtermore, hearing how much her death pained Yosuke. her new friend, is likely a reminder of the pain she felt the protagonist of Persona 3. For all her fears and insecurities over how "human" she is, she displays one of the most fundamental human emotions: empathy.
The story modes for each character give us the opportunity to find out how they really think of their teammates and of every interaction. And while this is the source of much comedy, it also has numerous adorable moments in each narration. Plus, P4A shows plenty of the interactions and feelings of the characters... without the protagonist around. In the games, most of the characters interactions goes, in a way, through the protagonist. But, in the first moments of the story mode, Yu hasn't arrived yet. That means that we get to see what the members of the IT act with one another (and not just in the obvious friendships, like Chie and Yukiko, but in cases like Naoto and Teddie).
Yosuke is doing his best as "second banana" in Yu's absence: just like in Persona 4 he is a source of cheer for his mates, but also the one who calls them to seriousness when it's time to work. When the Midnight Channel revives and rumours start spreading, Yosuke does his best to calm Chie and Yukiko down, both of them in different ways, and each girl's own narration shows that they really appreciate it. He is taking the mantle of vice-captain and doing pretty well, watching out for the team now that his partner is away.
Naoto's first reaction when hearing "Yakushima" is thinking how fun it would be to go there with everyone. During her narration, she makes it pretty clear how much her friends mean to her, that she is actually getting angry that a job is keeping her from enjoying time with the rest of the team, and even considers quitting!. When accepting the job, her condition was that she was not to abandon her school-life nor her home. She can't stand the idea of losing contact with her friends.
Kanji is convinced that the whole thing is a dream for almost all of his route. When hearing the harsh words that both Chie and Yukiko have for him, not knowing it's the enemy's trick, he feels bad for having that concept of them. And once he parts ways with Yosuke (running like a beast despite the latter's tries to talk to him), Kanji believes that Yosuke is leaving it all to him because he trusts him so much and has a nice moment of admiration for his senpai. Near the end of his route, he is thinking how his friends are the best and he is proud of being their friend.
After getting beaten in Yosuke's story mode, Chie asks him not to be so harsh when speaking to his next opponent. It's not just that she doesn't want her mates to feel bad, she is also letting Yosuke go with just that after hearing things that obviously hurt her very much and not even knowing he never said them. Compare that to the Chie who nutshot him in anger all the way back over a cracked DVD and didn't even look back.
Thanks to Naoto, Teddie realizes he really is the on who can understand Labrys' pain of not being human the better, and he does a great job at raising her spirits after her Shadow is defeated.
And, of course, how each member of the Investigation Team grows so fond of Labrys at the end of their story routes makes for some adorable moments.
Examples from Ultimax:
Ken truly does care about Koromaru, and one of his finishing poses has him petting him.
"Damn, out of time? At least Koromaru got some good exercise."
The end of Adachi's episode has him finally having that conversation that Dojima said they had in Golden's epilogue as he muses that such an odd bond might not be so bad.
The fact that he's trying to atone in the first place is heartwarming in itself, given that he was inspired by the Investigation Team.
Near the beginning of Adachi's story, he's pretty passive on the detectives' questioning and harassing him. Then said detective makes an insult toward Dojima. Adachi gets upset and proceeds to rattle the detective with sharp accusations and observations on the detective's past incidents. Adachi may portray himself as an uncaring asshole, but you don't badmouth Dojima.
While Labrys' Shadow side taking over when Sho tries to shut her down is admittedly terrifying, the heartwarming part comes afterwards. As much as she acts Ax-Crazy, when Yu and the others attempt a Go Through Me to stop her from killing Sho (they don't want one of their friends to become a murderer), she gives the original Labrys her body back immediately. Labrys realises that, as much as her Shadow tries to deny it, she actually fought Sho to protect her. Not only that, but she's able to use Asterius as her Persona (something that requires "strength of heart"), and refers to it as her "partner". All this indicates that Shadow Labrys is making aHeelFace Turn.
The "partner" remark in itself, as it makes them a Foil to Yu and Yosuke, who also use the term.
When Ken is protecting Kanji from his copy, he is reminded of something:
"As I raise my spear, the image of someone protectively standing in front of me resonates with me... from back then, and again just now."
While also being quite hysterical, the interactions between Theodore and Margaret, and how they talk about Elizabeth, show that the Velvet Siblings care for each other very much.
When Yosuke first brings up the possibility that Adachi could be behind the initial P-1 Grand Prix, Yu dismisses it out of hand since they knew the culprit didn't have a Persona or the ability to enter the TV World, whereas Adachi could do both. He notes in his internal monologue that his motivations for dismissing Adachi as a potential culprit are less because of the logical explanation, but more that he genuinely believes Adachi was being honest with his desire to reform.
Yosuke & Chie throwing themselves between Yu & Minazuki, as he suddenly strikes whilst Yu is off-guard after defeating Sho.
Labrys talks to Naoto about discovering what having friends feels like. Naoto can sympathise, since she was once cold and aloof before befriending the investigation team. Her internal monologue has a brief Not So Stoic moment as she reminisces.
During Episode P4, Yukari, Junpei, Teddie and Kanji stumble upon a reproduction of Labrys' personal hell from the previous game. Teddie immediately begins to worry for Labrys' physical and emotional well-being, with Kanji telling him to cheer up since being down isn't going to help either him or her. This scene really helps to illustrate how tight the bond between the IT and their non-human friends is.
Ken's reaction to Yukari being Feather Pink - he's practically squeeing whenever the subject comes up.
Quite a few of the character endings contain something like this. Standouts include:
In Yukari's ending, Mitsuru quoting the catchphrase from the opening of Featherman Victory to Yukari's surprise; before admitting that despite her duties as head of the Shadow Operatives keeping her busy, she still makes time to watch it because her best friend is one of the stars.
In Aigis' ending, Aigis and Yukari travel to Yakushima, specifically the facility where Labrys was created, and discover what's happened there since. Snowy, the dog that Labrys befriended, is still alive, and the testing chamber where Labrys was forced to kill all her sisters has become a beautiful garden.
In Labrys' ending, Labrys visits her mother. Or at least her grave, since the girl whose memories she carries died long before. But at the gravesite, Labrys meets a little boy who had the same disease that she did, but who has lived a longer, richer life because of the medical research conducted on her.
Any time Labrys is Aigis's navigator or vice-versa.
Labrys: "I dunno how to be a big sister, but I'll do my best!"
Marie is a DLC fighter, but one of her victory quotes reveals how much she's looking forward to seeing Yu again.