From the games, any Pokémon that evolves by friendship. After taking care of it for so long, it likes you enough to evolve from pure happiness.
An especially noteworthy example is Golbat into Crobat. Keep in mind that their lowest form, Zubat, is one of the original Goddamn Bats, not to mention it's not too terribly strong at first. But if you manage to raise one for yourself, it goes from one of the most annoying Pokémon of all time to one of the most reliable sweepers in the series.
Take a max-happiness Pokémon to Dr. Footstep and he'll tell you your 'mon's innermost feelings about you. They're usually quite touching and cute, especially if it's a "scary" Pokémon (like a Haunter or a Darkrai), or a "slow" Pokémon (like a Bibarel) that's grown sufficiently fond of you.
Most Pokémon: "<Name> is...a remarkable human and Trainer. That I can always perform the best any <Pokémon species> possibly can...I attribute that entirely to my partner <name>. When we travel, I can see wild Pokémon eying us enviously..." Scary Pokémon: "There are no Pokémon that dislike humans... Only humans that dislike Pokémon... We <Pokémon species> are especially shunned... But <name> always treats me as a friend and partner..." Slow Pokémon: "Hnurrr... Me? Uhm... Other Pokémon, they say to me... "You're not thinking, are you?" How insulting they should say so. It isn't true what they say. Think, think, think, I do that. All the time, I think hard how to help <name>. I concentrate! Hnurrr..."
Other Pokémon: "If I said there can be friendship between Pokémon and people, will <Pokémon species>'s friends understand? But if you see <Name> and <Pokémon species>, you will understand. Because <name> and <Pokémon species> are friends!"
This especially applies to Legendaries, since many of them have a Base Happiness of 0 (which basically means they hate you from the moment they're captured). You have to put in extra effort to max out their happiness, but seeing a Pokémon like Giratina or Darkrai give you nothing but the highest praise is VERY much worth it.
The player’s mother encouraging him/her at the start of the journey.
Manga
While the Ono Manga The Electric Tale of Pikachu has a lot of fanservice, it also has a great epilogue, that shows... well, a picture is worth a thousand words.◊
Volume Five of Pokémon: Diamond and Pearl Adventure! has Cyrus manipulating Hareta to the extent that one of Hareta's friends (a pawn in the plan) tries to kill herself. When Cyrus gives his evil tirade, he explains that the only true emotions of humanity are "hatred, jealousy, and burning anger", and gloats when Hareta unleashes fury against Saturn's Rhyperior. He caps off his speech with "You must hate me even more now." Hareta's reaction? SOBBING. He tells Cyrus "You do bad things, but I don't hate you," and talks about how he still wants them to battle someday. Cyrus is in disbelief and is nearly overcome, starting to save Hareta from the explosions (the building is blowing up around them them the whole time). Saturn stops him from going back in, but Cyrus leaves a Master Ball for Hareta just the same. Later, it's revealed that even though he got to the Spear Pillar first, Cyrus waited several hours for Hareta to show up. That reawakened human side is key in Cyrus's redemption in later volumes.
Others
Within the franchise concerning the original Red/Blue games, its said that Mewtwo starts to lose all its violent tendencies◊ once captured and raised by Red with kindness. Considering the powerful psychic Pokémon had such a traumatic creation, countless painful experiments performed on its body, and wandering the world angry and alone, its immensely satisfying to know it finally made a friend◊, and has a happier future.
Some extra Team Rocket Heartwarming (they sure do it a lot): In one episode, James nearly gets himself killed by trying to capture a rare and powerful Pokémon on his own, and while Jessie comes to rescue him, they both end up getting trapped by the raging Pokémon. Resigned to the fact that they're going to die, Jessie tells James that, if there's an afterlife, she wants to meet him again there. This actually makes the terrified James smile, knowing that he and his best friend won't separate even in death. Luckily, they end up getting saved by Meowth, but still.
Even sweeter because Meowth and Jessie, discouraged by their bad luck, had just abandoned James to go pursue careers. He was extremely upset, but as soon as they found out he was in trouble they ran to rescue him. Then they teamed up again. Status Quo Is God, but still, awww.
Anything where Pikachu almost dies and Ash saves him and they end up hugging.
On a video of "Emotion" from B/W, a YouTube commentator (by the username JTpiano24) commented about what Pokémon taught him. He said that Red taught him to not fear adventure, Gold taught him to not be afraid of change, Ruby taught him to not tamper with nature and let it run its course, Diamond taught him to not use religion to rule over others, and lastly, B/W taught him that beings had emotions, and that people needed to accept others to achieve peace.
This comic titled "It's The Thought That Counts which is about a Quilladin who has a crush on a female Braixen. The idea of this sounds cute, but each attempt to charm her doesn't go well for him. But the real heartwarming moment of the comic is how it ends.
Ever feel sorry for Trubbish and Garbodor, two of, if not the most hated Pokémon in Gen V, or perhaps the entire franchise? Don't worry - Bogleechhas you covered in this excellent article. For bonus points, read the comments below the article and check out how many people agree.
There's also this◊ piece of artwork (drawn by Deviantart user Pettyartist) featured at the end of the article, which serves as the perfect closure to it. People do care about you, Trubbish and Garbodor. The image also becomes Heartwarming in Hindsight considering how positively the franchise has portrayed the line, with Pokémon Sword and Shield having the best example in it being the only non-Gen I or Gen VIII Pokémon to get a Gigantamax form and said Pokémon being the signature companion of a woman who grew up in poverty with it as her only friend for the longest time.
The Japanese trailer for Sun & Moon A Japanese boy moves to Hawaii and struggles to fit in with his new home, but gets a chance to bond with a fellow classmate using their Pokémon games.
The fact that the creators of Pokémon designed regions designed on the two other biggest fandoms of the series (Unova=United States and Kalos=France) shows that they care about their fans.
During the Pikachu Carnival Parade on August 12th 2017 in Yokohama, Japan, a Mimikyu joined in the massive Pikachu Parade, receiving all the love it ever wanted.
More on the second example: it depicts a shiny Eevee, abandoned by their mother for being shiny and struggling to survive in the wild. Then a trainer takes them with him, and shows them nothing but kindness, and they eventually evolve into a Sylveon.
When rumors that the morale at Game Freak has hit "an all-time low" following the controversy that Sword & Shield generated (National Dex being dropped, leaks and cancellation of the game launch event in Toyko), fans got together to get the hashtag "#ThankYouGameFreak" going on Twitter. They succeededinto getting ittrending worldwide. That goes to show how much the fanbase cares for the franchise and the people working on them, even with all its ups and downs.
Even the staff at Game Freak took notice of the hashtag going viral, including Pokémon artist James Turner and Sword & Shield director Shigeru Ohmori. Their responses are just heartwarming.
From the fandom side of things, one Reddit user reveals that as a child, they used to spend hours breeding and releasing Lapras because the Pokedex said they were an Endangered Species. Even better, one commenter points out how Sun and Moon reveals that Lapras is no longer endangered, prompting another to respond with "This kid singlehandedly saved the Lapras species".
2019-2020 has been a very generous period for Porygon and its evolutions. Pokémon Masters EX included Porygon in as a feature called the Poryphone, who's role could've easily been filled by Rotom. After the line had been excluded from the base release of Sword & Shield, they were added back in through The Isle of Armor, with a Porygon given for free by Mustard's son Hyde, and Porygon2 having a giveaway event by code during late August 2020. Finally, the line was the featured Pokémon for the September 2020 Community Day in Pokémon GO. It also got a Spirit in Super Smash Bros. Ultimate.
To commemorate the upcoming release of Sword & Shield's Crown Tundra, Pokémon and popular Japanese rock band, Bump of Chicken work together to release an official animated music video, ''GOTCHA!''. Featuring familiar characters and Easter eggs from the past 25 years that truly hits a nostalgia to all Pokémon fans watching this video.
Special mention goes to Professor Oak's expression as he watches the protagonists (ostensibly meant to be us) at the end. It pretty clearly says "So Proud of You".
Partway into the song, we see the champions all get a moment to look awesome with their Pokémon - except two. We only see Alder and Iris' hands as they give each other a high-five, which serves as a heartwarming reminder how Drayden and Alder worked hard with Iris to help her legitimately earn her role as Unova's current champion. Ostensibly, this one gesture serves to communicate Alder Passing the Torch to his successor with full accolades.
In late 2020, Uri Geller apologized for launching a 20-year lawsuit against Nintendo regarding Kadabra note a Psychic-Type Pokémon that was based on him and his iconic Spoon Bending. The Japanese name Yungerer is a corruption of the name Uri Geller which caused the Pokémon to be unofficially banned in other media like TCG and the anime, and gave his permission to allow Nintendo to use Pokémon again. The heartwarming part was the people who persuaded him. It wasn't fans writing hate mail demanding Geller to rescind his lawsuit (as there's No Such Thing as Bad Publicity in Geller's mind); it was his two granddaughters, Liya and Romi, who made him realize that Pokémon made Kadabra as a positive tribute to him and his lawsuit had a negative impact on children across the world. Which is beautifully poetic considering that he initially feared that Pokémon would make children think he's an evil occult monster. Instead, Pokémon and children brought an end to a long-term ban with positivity and inspiration.
January 2023 had Pokémon's Youtube account post a video celebrating that as of Gen 9 there were now over 1,000 Pokémon. Every one of them is shown in the sprite or model they debuted in, and were shown in groups that they had in common. All to a nostalgic medley of tunes across the series.
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