Heartwarming / We Are All Pokémon Trainers

Unmarked spoilers below.

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J-Team Assemble Saga

• When Gamer's Serperior, who was killed in the fight against David, comes back to life as a Duskull. Writing that made the author himself feel all fuzzy inside.
• Jane getting reunited with Spoons the Ampharos. Spoons the Ampharos is an Ampharos who is Jane's closest and most trusted friend, the source of all Sweet Dreams Fuel, and a walking energy core for Incorruptible Pure Pureness. And she had been missing for an entire week.
• When DS starts feeling nervous about going to Unova without her team and wondering if she will still be a good enough trainer for whatever Pokémon she may catch in the Unova region, DS' Sinnoh team comforts her and reassures her that everything will be all right.
• Ribbons finally getting to meet her mother when the group arrives at the Pokémon League.
• A good portion of the team glomping Jane after she comes back to life.
• And before that, there was the moment between Wolf and DS when Wolf comes back to life.
• Portales finally meeting his old friend from the Celestial Tower again.
• Anom coming back from the dead.
• Keldeo's reunion with his long thought dead father: Keldeo the First.
• DS bringing a brainwashed Kyurem back to its senses by giving it a scarf, and Kyurem referring to DS as his friend afterwards.
• There are many of these moments between Wolf and DS.
  • Pretty much anytime that Wolf tries to protect DS from harm or supporting her during tough situations.
  • While the two of them are having a conversation in Nimbasa City, DS brings up the time Wolf kissed her in Opelucid city. Wolf freaks out a little when he realizes that was DS' First Kiss, and that he not only kissed her with no warning in front of everyone, but also that he was currently female at the time. DS assures him that she doesn't mind that he did so, and makes Wolf feel better by telling him about how she felt during the times he saved her from her inner demon in the Dream World and during his Disney Death back at the Pokémon League.
  • When DS learns that Wolf got heart swapped with Anom, she realizes that this is her chance to help Wolf the same way that he always helps her. However, this is easier said than done since they can't spend much time with each other around the others in the group (who don't know about the switch) as that might raise suspicions. Despite this, DS decides she can't just do nothing, and sits down next to Wolf-in-Anom, placing a hand on his shoulder. Wolf is very grateful for this small gesture. Later that day, they also manage to sneak away from the group and have a moment to themselves.
  • When DS accidentally blurts out Anom and Wolf's secret to the group, she refers to Wolf as "the person she loves", much to his surprise. When Wolf asks her about it shortly afterwards, DS confirms that she does love him, much to his delight.
  • DS kissing Wolf after he and Anom are finally returned to their own bodies, and staying by his side for the rest of that night and most of the day after that while he's recovering from the injury his body had sustained earlier.
• The first thing Jane does when learning that Anom is most definitely not dead? She hugs him until the cows come home. And he hugs back.
• Most of the group doing a group hug after Anom and Wolf's secret is revealed.
• Jane forgiving Groudon after he explains the reason why he couldn't help her all those years ago.
• Some of the trainers reuniting with some of their old teams after returning to Sinnoh.
• Slouch discovering that he has a fan.
• Everyone is sad when Jane is leaving to help June the Camerupt.
• A's expression of gratitude.
• Crush and Quetzal who were friends in their previous lives, meeting again for the first time since being revived from their fossils and the moment between them as they recognize each other.
• When Nadia the Salamence is finally able to fly again and the first thing she does being flying over to Lake to cheer him up after Luke lost his battle against Tagg in the tournament.

Upheaval Saga

• The reunion between Luke and Lake in the AU arc.
• Kamina nursing a sickly, orphaned Ducklett back to health and giving her a Name in the AU arc.
• Tangent reuniting with Basket and regaining his memories.
• Unite reuniting with Woolly.
• Celestia reuniting with Helios in the AU Relic Castle.
• Mezzo and Every confessing their love to each other during the AU.
  • And right after that.
• DS invoking The Power of Friendship in order to activate the Lustrous Orb and free Palkia from her petrified state.
• Dialga and Palkia reuniting after Dialga is restored to normal after the final battle of the AU arc.
• There are several of these after the timeline returns to normal:
  • DS' overjoyed reaction to seeing Sinnoh back to normal, as well as seeing her Unova team again.
  • Artemis reuniting with Mira after the latter is restored to life.
  • Stratus' happiness upon realizing that he can finally fly properly.
  • Many of the trainers reuniting with the Pokémon they didn't have in the AU.
  • Dialga, Palkia and the Lake Trio reuniting with Arceus and helping him out with his paperwork.

Aftershock Saga

• Crewe's releasing of Ashes
• Jab decides to invite the girl he likes out. Crewe says YES!!!!
• Chloro's forgiving by Magellan, right when she's about to kill him. They then hug and become a couple again.
• On Route 111, Mezzo becomes unusually sleepy, and both she and Every suspect something bad will happen if she actually falls asleep. Every stays awake and standing the entire night, supporting Mezzo to make sure she doesn't fall asleep.
• Tangent's memory reel following the defeat of Pokefutures!Tangent inside his mindscape.
• Following the end of Tangent's mindscape, Teala the Druddigon starts feeling a bit down after seeing her insecure aspect, but Zoltan helps her feel better.
• Umbramatic's reaction after his Sableye, Styx, reveals she's his sister Back from the Dead.
• Sierra reuniting with Rayquaza!Vyvyan after he escapes from Team Ozone.

Paths Saga

• Eskay and Psyche getting together in Unova during PMD-R, when Psyche woke up after a flashback nightmare from when she was abandoned by her father.
• After tying in a tourney in Bluescale, Nadia lets Spectrum keep the prize - the scarf AU!Lake wore. Spectrum then gives it to Skye as a late birthday present.
• Maekrite telling Teala he still likes her even if they can't be mates.
• Rex talks to Teksab about the power of friendship.
• Ho-oh himself tells Skye that she's still significant, even without a Heart of Gold.

Cipher Saga

• Lyuri and Duke have both said that they aren't very fond of Interspecies Romance. That didn't stop them from getting together.
• After losing to Pallad, Jacob — who had been incredibly awkward with any sort of affection prior — wants nothing but comfort from Lity.
• After an entire day spent on deciding on what to do for a date, Lyuri asks Duke if he truly loves her or if he is just being her boyfriend to make her happy, Duke decides to Take a Third Option and elaborates on it, they then do one last thing together before calling it a day.
• Wolf semi-proposes to DS.
• After six years, Ivy returns to Eskay with the former barely saving the latter's life.
  • Eskay's first time conscious after the reveal continues the Heartwarming-ness.
• Everybody cheering Sakura up after Verax almost shoots her dead, even the ones that had barely any interaction with her, should count as well.
• Tesse and Sam proclaiming their love for each other.
• After all the blackmail, paranoia, corruption and attempted crimes, Lyuri and Duke finally reunite.
• After a Tear Jerker in which Crewe regains her memories after being purified only to realize that she had fatally wounded Straw moments before, Mew (the one from Crewe's backstory) shows up and decides to bring Straw back to life upon hearing Crewe's pleas for her to do so as well as the other trainers present showing confidence in Mew being able to do without messing something up. And it works!
• Pi comforting Joseph after the latter was nearly murdered by Kyrie. It includes this exchange:
  Joseph: "Sorry to trouble you..."
  Pi: "No. No. You are no trouble. You are never trouble."
• DS admitting to Tagg why she came with him for his confrontation with Tokarev shortly after Tagg saved her life, giving up his chance to kill Tokarev to do so.

Recovery Saga

• Eskay is revealed to be male-to-female transgendered in the main timeline, and decides to go through with the full conversion, informing Pent of it beforehand.
• Herbert's letter to DS in an effort to repair the rifts in their friendship.
• Ever finally coming to terms with what happened in Orre.
• Valentine's Day 2015 is chock full of them, including but not limited to:
  • Eskay and Lucius's last hour of the day together.
  • Umbra and Chrome not having any ideas for a Valentine's gift, only to be ambushed by their respective significant others (who are bearing video games).
  • Blitz and Sakura's gift trading.
  • Dune and Deziree's trip to the Lavaridge hot springs, where Dune reveals to Deziree that it's also her birthday.
• Nico and Maggie's talk following the defeat of the Shadow King.
• Ludmilla finding out she's been adopted by Dune and Deziree.
• Lane talking to his father, Arthur, after he showed up as Ignia's Alola League Champion fight. The exchange brought tears to Lane's eyes and inadvertently got his author sniffling too.