- The player rescuing their starter from the Chrysalimon at the start of the game then, when Yuugo shows up to save them, teaming up with their starter instantly to fight off the rogue Digimon. This act was the first time in the history of EDEN of a Digimon willingly partnering with a human or a human getting a Digimon partner without the Digimon Capture program.
- Nokia is absolutely terrified in the first visit to Kowloon because she's afraid of Digimon which she believes to be malicious computer programs. Then she drops it completely when she meets Agumon and Gabumon. Then, when Eater attacks the group, Agumon and Gabumon team up with the player's starter to Hold the Line so that Nokia and her friends can escape.
- After the incident, Nokia hires the player to take them back to Kowloon because she's afraid something bad has happened to the two Digimon who saved her. She's absolutely terrified and constantly being pestered by hackers but she stands up to them, despite being unarmed, just to protect her Digimon friends.
- After the fight is interrupted by Yuugo and Fei and Jimiken leaves, Fei tries to use the Digimon Capture on the two Digimon. Yuugo stops her, saying it's not worth it.
- After she starts her hacking group, the Rebels, when facing a Black WarGreymon and Black MetalGarurumon, Agumon and Gabumon warp digivolve to back up her feelings for them.
- Several of the side cases that involve Digimon and humans either working together towards a common solution or becoming friends in some way.
- In one side case a Minervamon is posing as a human girl while talking to a teenage boy. She isn't doing it out of romantic intent, but rather because she likes talking to the boy and wants him to feel like he has friends. She listened to his woes about how his family life was going down and he was too nervous to talk about it with anyone else and then gives the player advice to give to his mother, who understands now what its been like for him and will make an effort to reconnect. It's a heartwarming end overall.
- In Chapter 13, a little girl named Fuuka made friends with an Elecmon and Numemon after the digification. Her brother, Masanori, is paranoid over her going out late and accuses them of using her until the protagonist points out she's having fun and he agrees to let them continue playing. When she nearly gets attacked by a Cyclonemon, Numemon and Elecmon immediately try to protect her against a digimon far stronger than them.
- A rather simple side quest late in the game has the player buy a blanket for a girl who wants to give it to a Metalgreymon out on the streets because she thinks he's cold. It turns out he just has blue skin, but he is still touched by the gesture and asks you to tell her thanks by giving her an old music box in return that makes her feel warm inside and eases her sorrow about leaving her friends behind when she moves away the next day.
- Reiko Tawa at Shibuya records employs you at one point to figure out why mysterious albums are appearing in the store with weird markings and awful music on them. You find out the culprit is an Etemon who just wants to spread his music. Rather than kick him out, Reiko and Etemon bond over music and become friends. It helps that they each turn out to be a Dreadful Musician.
- After Reiko mentions liking his music and theorizes that she might end up the president of his fan club someday, Etemon actually has to turn around so she and the protagonist don't see him crying Tears of Joy over actually having a fan.
- Comes to a head late in the game when Jimiken kidnaps Reiko to force the player into a rematch with them. Etemon becomes furious, worried for Reiko's safety and this causes him to digivolve to his mega form, MetalEtemon to join you in battle. Thankfully the whole kidnapping turns out to be a ruse.
- Sorcerimon has been helping patients since he came through the portal since he couldn't just sit still while others were being hurt.
- A Growlmon is worried about his hacker enough to have the detective agency intervene and help him make Ramen for her. She breaks her diet to enjoy it, to both of their delight.
- When humans and Digimon come in contact, especially later in the game, you'd think there would be a lot more chaos. But many of the Digimon are fine with the humans. Many of them are very friendly and try and help out. In fact, if not for the world ending scenario and the machinations of a few Digimon, they might almost be able to live together easily. One case has a hacker attempting to use a Digimon to fight, with the Digimon objecting and the hacker, confused, asked what he does want. It turns out the Digimon just wanted to be friends.
- In a DLC case, a Rosemon, Blackwargreymon and Myotismon are almost tricked into being villains in a super hero action movie made by a group of self proclaimed "Justice Warriors". The "heroes" say that they should be villains because they look the part, but don't even ask if that's what they want. After you beat them, the "heroes" apologize for hurting the "villains'" feelings, after which they all agree to make the movie together.
- Before the player Connect Jumps into Eater Eve to save Yuuko, Fei laments that she can't go and save Yuuko herself. Fei's Digimon, Tigervespamon, appears before her and says that they will go in her place. Fei is baffled by this because she always thought that Digimon were just tools for hackers to use and thus starts to realize that they are living creatures with feelings just like humans.
- When the player Connect Jumps into Eater Eve and Eater Adam to save Yuuko and Arata respectively. The two are wallowing in their own emotions and insecurities while trapped inside, but the player snaps them out of it to show them that You Are Not Alone and takes their hand to lead them home. Or in the case of Arata, give them a punch to the face.
- After the Digital Shift that allows Digimon into the real world occurs, your first case actually comes from Makiko Date. She wants you to help a wayward Lopmon find her friends. It really shows her Jerk with a Heart of Gold tendencies at their finest and after you help her, the texts she sends you are a lot more friendly. Mostly because she stops threatening to arrest you all the time.
- The conclusion to Pete's story. He's reunited with his beloved master and the two leave to spend the rest of eternity together. It's suggested that they may be Dead All Along, but Kyoko and the player decide not to pry into it.
- After the player's digital body finally falls apart after the final battle and they remain in a coma, Nokia gives a monologue to the sleeping player and then sets off with Arata to find their friend. Nokia and the others are determined to keep the promise they made and bring everyone home safely.
- After the player's body falls apart and their data is scattered, they awaken in the digital shift between the real world and digital world to see Alphamon!Kyoko explaining to them what happened. Your Digimon, the ones that you raised and cared for, gathered your wayward data to put you back together. You then spin around in a first person view to see all of the Digimon that were in your party at the end of the game surrounding you as if to give you one final farewell. Though this can cross over into a Funny territory if your party was filled with more hideous and goofy Digimon like the Numemon line.
- In The Stinger for the game, the player meets the real Kyoko in the real world. The player is seen with a cup of coffee and a bottle of mayonnaise to which she comments on how it's an odd choice for a blend. This suggests that either the player actually grew to like Kyoko's weird, Lethal Chef blends over the course of the game or that the bizarre blends are just what they use as a means to remember their friend.
- Kyoko then asks the player if they've met before because they seem familiar before offering them a job as her assistant. It seems that despite having technically never met, their friendship has persisted. The player smiles and the game ends
- Just after beating the final boss, the protagonist is about to risk their own existence to try for an Everybody Lives ending. The protagonist's friends try to convince them not to go through with it, but Kyoko-Alphamon simply tells him/her to find the truth as a Cyber Sleuth, the way only they can.
Heartwarming / Digimon Story: Cyber Sleuth