Meowth's backstory is sadder than sad. No wonder he wants to rule the world.
Mystery at the Lighthouse, a gigantic Dragonite is lonely and desperate for friends. It comes to Pokemon researcher Bill's Lighthouse in the hopes of making one, but is driven off by a terrified Team Rocket. It moans sadly and disappears back into the fog, never to be seen again.
The end of the Indigo Conference arc. Watching a recap of Ash's entire experience of all the battles he went through, all to the glorious sound of the Pokémon Theme. It makes you feel like he really did give his all to get as far as he did. You feel proud that he did so well. And afterwards he stands in the middle of the stadium, and reasserts his vow to become a Pokémon Master. The Pokémon League may be over for Ash, but his journey has only just really begun.
The climax to the first episode, "Pokemon, I choose you!" Try not to get a knot on your throat when you see Ash eager to be pecked to death for an insubordinate Pokémon he only just met.
Pokémon episodes "Pikachu's Goodbye", "Bye Bye Butterfree", and "Charizard's Burning Ambition". Probably other episodes too.
For some, it's not so much the episode as the song "The Time Has Come (Pikachu's Goodbye)" from the Image Song CD. You can listen to the song here, if you don't mind tearing up.
If it was even possible, 4Kids did manage to make the first two even sadder than it was originally (the dub opening was surprisingly effective in making Butterfree's departure dramatic). "Pikachu's Goodbye" also had a Crowning Moment of Heartwarming at the end of the episode.
Butterfree's goodbye was recycled ten seasons later with Jessie's Dustox. Didn't have the music making it sadder, though, the way "Bye Bye Butterfree" is.
The original has the first movie's theme, "Kaze to Issho ni", playing over the release. And let's face it — it's the first time Jessie's broken down like this. Watching her crush Dustox's Poké Ball under her foot in tears is heartbreaking, and a rare soft moment from the Team Rocket trio's leader.
Misty releasing Togetic. Especially when you think of it from the standpoint of Misty being a mother that has watched her 'child' be born, grow up, and then reaches the moment where she has to let go and release that child into the world to live independently of her.
"Togetic... I love you."
The entire first episode of Charmander's appearance. Just picturing it freezing and shivering alone on that rock during the rain storm doing it's best to prevent its tail flame from going out, and essentially killing it is one of the saddest moment of the series.
The end of "Charizard's Burning Ambition" was heartbreaking, because the way Ash left Charizard said, "If I stop, I'll change my mind."
Tepig's background story is just as bad. After Tepig loses a battle, his trainer abandons him in a rather cruel way; the porker is tied to a fencepost and forced to watch his trainer walk away on him. To make matters worse, he still loves his trainer; Tepig literally breaks down into tears and tries to chase after the guy. Before Don George can free him, however, Tepig shoddily bites through the rope and promptly sets off to find said ex-trainer. Oh, and some of the rope gets caught around his snout. When Ash finds him, Tepig is on the verge of starving to death.
Charmander's story in general is quite sad, though it does get better. It was good friends with Ash, but when it evolved, it suddenly became hostile and aggressive, which got worse when it evolved into Charizard. However, at one point, it is weakened during a battle, and Ash spends the entire night trying to keep it warm, getting blisters all over his hands in the process. The next day, for the first time, Charizard fought for Ash.
Some people can't watch the prequel short on the Mewtwo Returns DVD without crying, and tears up just at the sound of "Chiisaki Mono" from the sixth movie.
The short in the first movie can also be quite hard to see, especially with young children. Watching Charizard screaming and thrashing about while trapped, and then seeing his utter despair as he realises he can't free himself is pretty heartbreaking. Of course, the it turns into a different sort of tear jerker as all the other Pokemon work together to save him.
During the second movie, Team Rocket's attempt at Heroic Sacrifice when they let go of Lugia so as not to slow him and Ash down. Their "last lines" are just too priceless: "Let's not say goodbye/Let's just say/We're gonna die." Of course, they live, but still...
Don't forget their variation on their usual send off as they fall: "Team Rocket's blasting off for gooooood...!"
The scene in the 8th movie where Lucario sacrifices himself to save the Tree of Beginning.
Also, during the aforementioned scene when Lucario discovers that Aaron only trapped Lucario so that he wouldn't follow him and suffer the same fate. And during the ending credits, Lucario and Aaron eating the bar of chocolate Max gave Lucario earlier in the movie.
Celebi's "death" in the fourth movie. Ash and Sam's reactions were bad enough, but seeing Celebi's shriveled, lifeless body pushed it over.
Also from Movie 8, Ash calls out all of his Pokémon as he's being absorbed by the energy orb-gunk and, in the dub at least, he says goodbye to Pikachu and tells him he loves it as he gets fully absorbed. The sight of Pikachu and all of Ash's Pokémon at the time crying, including Grovyle(!) was like "Mewtwo Strikes Back" all over again. Then when Ash, and everyone else comes back, Pikachu, with tears in its eyes, hugs Ash. Then Ash gets glomped by Phanphy and Corphish while Grovyle and Swellow watch.
Ash: Pikachu, you can't save me! Just take care of yourself, and all the others! I'll miss you, buddy. I LOVE YOU!
And just the way he says it all as fast as he possibly can while still being coherent. Just knowing that you have about ten seconds to say everything you need to, to say good-bye...
The beginning of the episode "Gotta Catch You Later" where Ash, Misty, and Brock separate after being together for so long is pretty moving.
The farewell of Misty in the Master Quest season.
Everything about that first half of the episode. Misty's sad look when she realizes she'll have to go home. How upset she is when Ash, not realizing the gravity of the situation, just comments that she has her bike back and can get home faster...then her walking away crying, thinking that Ash doesn't seem to care that they have to split up. Then Ash and Brock show up to help her battle Team Rocket...Ash compliments her on her battling and Misty, instead of brushing it off like usual, thanks Ash and says it's "sweet" of him to say. About the only thing the dub missed was the fact that in the original, Misty tells the eternally-dense Ash, point-blank, that "it was never about the bike"
It was also the last time the original cast traveled together. In the Kanto Battle Frontier, May and Max were with theYm, and Misty never rejoined Ash and Brock alone, and with Brock having been Put on a Bus after Diamond and Pearl, they likely will never reunite for another adventure. The Fellowship Has Ended indeed.
Brock returned to the anime for the final episode of the Black and White/Best Wishes series. Many veteran fans rejoiced when this happened. Word of God says that he could return for the X and Y series.
Larvitar's backstory in "Address Unown". The poor little mon can do nothing but watch in its egg as its Tyranitar mother is injured by the poachers who kidnapped it, leading it to be afraid of humans when it hatched. And later on the memories are too much for it, represented by Larvitar essentially being frozen in an ice crystal. It's followed by what is considered to be for some, one of Ash's biggest Crowning Moment of Awesome: his heartwretching I Know You Are In There Somewhere Fight to Larvitar.
In the first movie, Meowth's clone telling Meowth that they don't have to fight. They have a lot in common: the same earth, the same air, the same sky. If they could look at what's the same instead of what's different... well, who knows.
The first movie (the above picture) when Ash is dead, and Pikachu goes up to his body and tries again and agiain to wake him up via electrocution, until it's out of energy and can do nothing but cry and then the other Pokémon, not only Ash's, but the trainers' Pokémon and Mewtwo's clone Pokémon, cry also. He gets better, but it doesn't make it any less sad.
What makes Pikachu's actions even worse is the implication behind them. He's turning himself into a living defibrillator, and it's not working. Possibly doubles as Fridge Brilliance.
Just listen to the music "Tears of Life" from the movie and see if you don't visualize the scene mentioned above and start sobbing hysterically.
The Tear Jerker song If Only Tears Could Bring You Back by Midnight Sons represents this scene in the CD.
"If Only Tears Could Bring You Back" might also sum up Mewtwo and Amber as well, from the Mewtwo's Origin short that was cut out from the movie's theater release.
The biggest punch, though, is Misty's reaction. Ash has been harmed in many ways throughout the first season, but a Pikachu shock always revived him, and Misty and Brock just laughed and moved on. After Pikachu's attempts to revive Ash fail again and again, and the believed finality of Ash's demise hits both the characters and the audience, the mood of the scene continually drops, until all Misty can mutter is a pained, "Please, no." It's the only major human reaction we see, and the only one we really need to see. Sure, the Pokemon crying is touching to our childhoods, but looking back as adults, it's clear Misty speaks not only her voice but the voice of the audience. "Please, don't let it end like this."
For some, it's James' farewell to Chimecho. His line in the dub "It's just...I don't know how to deal with this" Some of the same people also tear up every time when they see the scene where May tears up after losing the Kanto Grand Festival
Speaking of James, some people still can't get through 'Holy Matrimony' without bawling like a little kid. James telling the story of how he froze to death as a little kid after running away from home, with his Growlithe watching helplessly at his side (the fact that it was obviously fake doesn't make it any less sad) is already tear-worthy, but at the end when he's forced to leave Growly so he can rejoin Team Rocket and remain a free man is part heartwarming, part tear-jerking.
In a certain Johto episode, Team Rocket locks up Chikorita in a strong cage, making her unable to escape with Razor Leaf or any other maneuver. Team Rocket then proceeds to use its Pokemon to attack Ash. Chikorita is forced to watch her master, who she undyingly loves, be harassed without the ability to stop it. You can even see her eyes well up with tears. She evolves into Bayleef in time to save him, but it's still heartbreaking to watch.
The ending of "Pokémon Ranger and the Temple of the Sea" qualifies.
The Birth of Mewtwo. Especially when Amber/Ai, Young Mewtwo's best friend dies. Just the line "Don't cry, because you are alive! And life is wonderful."/"Live, all right? I'm sure living is wonderful." makes some tear up.
Amber/Ai:(Giggles) I think it's almost time for us to say goodbye. Mewtwo...live, all right? I'm sure living is wonderful.
Mewtwo:Ai..I..I'm in the glass...in the water, but water is flowing from my eyes...what is this?
Ai: (Giggles) That's probably..tears.
Ai: Papa said all living things don't shed tears unless their bodies hurt. And the only ones who shed tears because they're sad are humans...Mewtwo...
Ai: ...Thank you for your tears. But Mewtwo, don't cry. You're going to live. And I'm sure that living is wonderful.
Mewtwo:Ai, they won't stop...The tears..what should I do? Ai, answer me...
Mewtwo's entire life. He has to watch all of his friends die before he's even born, which is so traumatic for him that the scientists have to wipe his memory in order to keep it from killing him, too. Then, when he is given his first taste of the real world, he discovers that his entire reason for being is to have tests run on him, like a lab rat. Once he breaks out, he discovers that every other Pokémon is either in the wild or under the ownership of humans, who make the Pokémon do their bidding. He goes berserk at this point, and has to be forcibly taught that not all humans are bastards. He and the Pokémon clones that he created then go to live out their lives in a place apart from those who would harm them. But Giovanni comes and threatens to execute every last one of them unless Mewtwo submits to him, and has to be bailed out by Ash and company. The last we see of him, he and the Pokémon who depend on him are still hiding from humans, probably terrified that they will be found again. Can you really blame him for going berserk several times?
Well, maybe not quite in hiding. Mewtwo is alone the last we see of him, and one of his inner struggles in Mewtwo Returns was deciding to protect his clones, or let them go. In the end, he releases them to live new lives, whether in the wild or with a trainer. The last shot in the special of him gazing at the moon overlooking a human city is a powerful testament of how far along he's gotten in becoming more accepting of the world, and who he is. It also counts (possibly) as an Earn Your Happy Ending or Bittersweet Ending if you read more into the context.
Speaking of Pokémon, the capture of Pikachu by Mewtwo's evil Poké Balls in the first movie. Gets me every time. It's been established that Pikachu does not like being in a Poké Ball. Many times. Ash is beaten half to death by evil Poké Balls and robotic arms in a chase all over Mewtwo's fortress. He does all he can do to save his buddy, and in the end, he fails. Pikachu has been captured by The Big Bad, his freedom stripped away. He gets rescued, but still...
Related to Pikachu's Poké Ball phobia, Ash demanding Pikachu get into one in "Snow Way Out" so he won't die from the blizzard they're stuck in. As if to prove Pikachu's point that he won't leave his trainer's side, his other teammates come out of their Poké Balls and hug Ash...
Also from that episode, the flashback to Jessie's childhood. She was so painfully poor that a meal entirely made of snow was a delicious meal to her.
Latios' final goodbye to Latias, in the fifth movie. The way the now-translucent Latios takes Latias' hand, and then Latias realizes, confirmed with Latios simply nodding, before the two's grip breaks, and Latias is pushed away, this heartbroken look on her face......... It's really not helped by the scene a few minutes on, which shows the Earth/world e.g. what Latios is seeing, through his psychic connection with Latias, for the final time.
Especially since the creator of Pokémon always used the word "faint" to describe defeated Pokémon so that kids wouldn't have to hear about death. This makes the first on screen Pokémon death even more moving considering that Latios sacrificed himself to save his little sister Latias, and the town they lived in and explains in the games why Latias learns Wish and Latios learns Memento.
Just a small one from "A Scare in the Air," watching Jessie and James sit there mumbling "Looks like Team Rocket's messing up again."
The end credits to the third movie, partially because of the song playing ("To Know The Unknown"), and partially because of one scene that shows the return of Molly's long-lost mother.
Also from the third movie, the part when Ash is falling into the pit, and suddenly Charizard, the Pokémon that previously hated him and refused to ever do what he said, swoops out of nowhere and saves him.
Molly's parents both disappearing, one leaving her family, the other being dragged into another reality. Also, the whole part about rejecting her reality in favor of living in her dreams. The entire OST of the movie emphasizes the isolation and loneliness Molly experiences.
The entire "Team Shocker!" episode is a huge Tear Jerker. Dawn, the resident cutie is broken all of a sudden, after 2 lost appeals. Soon after, it cuts to a scene where her mom Joanna is shown disappointedly glancing at a wall full of photos of both her and daughter participating in contests. Next, Jessie goes and rubs her victory in Dawn's face. And Dawn later cries herself to sleep..
It was so upsetting that Ash himself was on the exact same emotional wavelength.
It's made even worse. For around a dozen episodes,the broken self esteem'd Dawn doesn't want to enter in contests anymore, thinks she's failing her Pokémon and tries to fake happiness.
The first time she loses the appeal round is pretty bad too, as Dawn runs outside and bursts into tears. It's also the very first time it's ever happened.
"A Poached Ego" gave us Team Rocket's Crowning Moment of Awesome at the cost of a few tears. TR comes across a poacher who has captured a bunch of wild Ekans and Koffing, the pre-evolutions of their main Pokémon: Arbok and Weezing. In an Even Evil Has Standards moment, TR attempts to free the captured Pokémon, but the poacher tries to stop them. In the climax of the episode, Meowth manages to free the Ekans and Koffing from their cages. When the poacher sends his Tyranitar after them, all three Rockets throw themselves at it. The battle is completely one-sided as the Tyranitar beats them mercilessly, all while Jessie and James are shouting at Arbok and Weezing to take the Ekans and Koffing and run far away. The fact that their Pokémon have tears running down their faces says just what they think about following that order, even if they do so anyway.
"Go West, Young Meowth". Meowth's backstory is indeed a sad one. He learns to speak human language, and goes through all sorts of ordeals in order to walk like a human, just to impress a girl of his species and the pet of a rich woman... only for her to reject him. Then there's the end of the episode, where Meowth stares at the moon still pining over Meowsie.
Then, if you still aren't moved by all the emotional moments Meowth goes through in the first parts of the episode, wait until you see what follows. Meowth meets Meowsie again in an Dickensesque pauper gang, and the viewer learns that her rich, loving owner set her loose when she lost all her money.
After the death of Maddie Blaustein in 2008, this episode became even more of a tearjerker than it already was.
The death of Maddie Blaustein is a Tear Jerker all on its own.
Odd Pokemon Out! has Grovyle falling in love with a Meganium after the latter heals him after he lost his battle with a Tropius. Grovyle goes off to fight Tropius again, this time defeating it, and spots Meganium running towards him. He expects that she was going to congratulate him... but she doesn't. She runs straight past him to Tropius, heals him, and then nuzzles up to him, which was when Grovyle found out that Meganium never loved him, but she loved the one that kicked his ass earlier. Ouch.
And not too long after that, he evolves into Sceptile, only to be unable to use any of his moves. It was a real kick in the face watching Team Rocket's Pokemon knocking him around like it was nothing.
In the 10th movie when Darkrai couldn't block Dialga and Palkia's attacks anymore and they strike him, which ends up killing him. Thankfully, Palkia is able to restore him along with everything else at the end.
Darkrai's (and no doubt by extension all Darkrais') backstory. Being reviled by everyone just because you have a power you can't control...
Considering what he does is basically an uncontrollable self-defense mechanism... it is. Well, except that one Darkrai who almost succeeded at plunging world into eternal darkness. He gets better after his memory is accidentally wiped out, though.
In "True Blue Swablu", near the end when just as Swablu is about to join May's team on her journey, its family comes back. The music, May desperately trying not to break down and Max's questions about why she's letting Swablu go back to its family despite it wanting to come with their group in the first place.
When Lapras finds its family again, but they shun it because Lapras is with humans.
The first episode with Lapras being abused also counts for this trope.
The part when Ash had that crushing loss to Paul — the fact that Chimchar evolved into Monferno and tried so hard to pull another win for Ash and the fact that for the last bit of that episode you do not see Ash's eyes at all...
And then the next episode...Ash's in a depression. Not only has Paul defeated his pokemon, but his philosophy and beliefs in what brings out a strong pokemon. He has to watch all of his Pokémon get treated, then lays on the side of the hill, remembering the battle over and over and over. He was in a depression for a good 25 minutes of the episode! Not even GARY beat him that hard. Thank goodness his friends cheered him right back up, and good thing it was soon, because Team Rocket tried to insult him AFTER he recovered.
"Do I Hear A Ralts?" Plot: Max finds a sick baby Ralts by the side of the lake. He has to take it to a Pokémon Center but several things are getting in his way, including Team Rocket, the severity of the fever, and the distance to to the Center...but he clears all the barriers and manages to get Ralts to the Pokémon Center without knowing if it will live. The next day, it is completely cured, but has to be returned to its family, Kirlia and Gardevoir. Ralts does not want to leave Max, telepathically telling him to promise that he'll come back for it when he's a Trainer, and Ralts teleports away as the episode ends.
"Chiisaki Mono" (the ending theme for the 6th movie) Same for "One" (the ending for the 11th movie). "Soko ni Sora ga Aru Kara" has the same effect.
James having to give up Cacnea so it can learn Drain Punch. Sure it was a Team Rocket Pokémon that was often used as a punching bag for the protagonists, but you can't really help but root for the cactus Pokémon in his departure episode. Watching it being battered while trying to master Drain Punch can make some people tear up.
In the episode "Great Bowls of Fire", Dragonite snapping out of its Outrage only to witness the results of its attacks: the complete destruction of its peaceful forest home. Its tearful howls are pretty heartbreaking.
The scene in the twelfth movie where Arceus saved Michina from the meteor. You know he gets better, but seeing him lying there in the snow, with all of the other Pokémon cuddling up to him and trying to keep him warm... And then, when Damos uses his special ability to see the hearts of Pokémon, Arceus is just grey... like the rocks he's lying on...
It is worse when you remember what Arceus is. A creature akin to a god is dying. A god. Is. Dying.
And on top of that everyone from the future is fading - because they might not even exist if Arceus dies here! Ash is the last to go, and he just manages to get the Jewel of Life to Arceus before disappearing completely. Thank goodness the process is reversed with Arceus' survival.
Before that, the Big Badstarts his (modified) plan to kill off Arceus in the past, using its weaknesses to Lightning, Water, and now Metal. Seeing Arceus, at this point compassionate to humans, being ravaged by the attacks and slowly drowned in molten silver is a gut-wrenching thing to experience... and is no doubt intended to be seen as such.
The look on Ash's face when he finally brings the jewel to Arceus and fully realizes the state it's in. The poor thing looks like it's already dead, with nothing but a faint glow of red left in it's eyes.
The end of the Team Galactic arc. Saturn has remained his usual, cold, fierce self, but then stops Mars from going into the portal; and at the end when they're taken away, the fact that Mars, who had previously been extremely spring-loaded, occasionally bordering on annoyingly insane, was just so quiet and didn't put anything in to the conversation. Of course, that scene turned (sort of) into Nightmare Fuel with how coldly and fiercely Saturn tells Jupiter that Cyrus got away.
If you know (and sympathise with) Cyrus' backstory and believe it applies in the anime universe (the verdict's out on whether it does or doesn't), then it becomes even worse.
Mars' reaction when Cyrus tells her he'll be the only one in his perfect world. Once she puts two and two together, the way she screams and then she runs after him as the portal's closing. Saturn stops her from going in after him.
The final episode of the Diamond-Pearl series, "Memories are Made of Bliss!". Brief summary: " Ash, Dawn and Brock arrive back in Twinleaf Town, and while waiting for a ferry back to Kanto the gang become depressed knowing they'll soon be going their separate ways. While everyone tries to keep their sadness at bay, it proves to be too much for Piplup..." Piplup takes it very badly. Since the party just can't move from a region to another without splitting, there is no way this is gonna end well.
Piplup breaking down in front of Pikachu...indeed; the realization of leaving one of his best Pokémon friends became too much for Pikachu as well, and the Team Mom Togekiss has to comfort them both.
And while that's happening, this music plays, which in and of itself is a bit of a Tear Jerker for fans of the old seasons.
And if you watch the Japanese version, you see this tribute during the ending credits. It's a simple, but beautiful sequence which farewells Dawn and Brock from the regular series and reaffirms the series' themes of friendship. The song playing, In Your Heart, Lalala, itself counts as a major tearjerker, especially if you know the lyrics.
Lawrence in the end of the second movie. Sure he was greedy, but he never came across as evil, and to see him wandering aimlessly in the ruins of his collection only to find the one scrap left. He picks it up and stares blankly over the ocean. To add onto it, that collection of his was made of ancient artifacts. That's world history that just got vaporized.
The scene in Pokémon: Zoroark: Master of Illusions where Zoroark dies after risking everything to save and protect her baby boy, Zorua. To elaborate, Zorua has gone through an endless amount of pure crap and has gotten shocked to the bone, kicked around, and almost killed by the villain, and Zoroark has done everything in her power to protect him (and trust us, she is VERY powerful). And then she just can't take it anymore and falls to the ground, dead as a doornail. Thankfully, she gets better.
Made worse when Zorua spends the next few minutes trying desperately to wake her and finally bursts into tears. He then makes an illusion of their home, begging his mother to wake up so they can finally go home and be together again, finally ending by screaming his pet name for her at the top of his lungs, heartbroken. And even more, Ash's voice actually cracks with grief when he tries to wake her as well.
To add punch in a guts: in Russian dub Zorua calls Zoroark "Bulya" which is short from "babulya", Russian for "grandma". So, if she's his granny and he lives with her... then what happened to his parents? Given how desperate Zorua was to wake her up, it could only mean that his parents are dead...
Squirtle leaving Ash and rejoining the Squirtle Squad.
Probably one of the most overlooked moments in the entire series would have to be when Pidgeotto (now Pidgeot) leaves Ash to protect some wild Pidgey and Pidgeotto from a gang of Spearow led by a Fearow who evolved from the Spearow that Ash tried to catch on the very first day of his journey.
And then made even more sad by the fact that Pidgeot doesn't just leave. Ash makes it out as though it's a temporary arrangement, tells Pidgeot that he'll be back after Professor Oak's pokeball has been delivered, and waves it off cheerfully, calling out that he'll see it soon. He never comes back.
The "Fly Me to the Moon" episode. Period. Ash & co. find a trainer with a Pidgey called Orville, who is the only one in the entire island who can fly. He wants to fly in the sky higher than any other Pidgey did, and reach outer space. Ash & friends (and more importantly, Team Rocket) help him, and obviously he achieves his goal...But when he reaches the atmosphere, he's already freezing, and without oxygen, on the verge of death....Meowth, who is translating what Orville says through a communicator, says that Orville told "he has never seen something so beautiful" when he sees the Sun from the atmosphere. Meowth then pleads to Orville to get back to Earth before it's too late, and the Pidgey falls from the skies in an unconscious dive.....He gets better, of course, but to see the self-sacrifice of the Pidgey to achieve his dream almost reducing even Meowth to tears was...oh dammit...
Meowth's pep talk the night before Orville takes flight.
Meowth: It's okay, pal. Meowth is here to help ya! Once upon a time, Orville, I was just like you. I yearned. I yearned to rise above other Meowths. Nothin' was ever gonna stand in my way to learn to talk human talk. Y'see where I'm goin' with this?
Meowth: I understand what you're goin' through, pal, and I wanna help you, cause nobody was there to help me. So I'm gonna be flyin' alongside ya, as far as this here balloon is able to take me. And with this mini micro walkie-talkie, I'll still be able to stay in communicato with ya. ...This is too important to blow! Pokemon need to hear this! You will be a hero! When they see what we're capable of, all Pokemon, big and small, will make their own dreams come true!
Meowth: For the Pokemon!
Pokémon the Movie: Black/White — after trying so hard to get Victini free, those pillars clouded around him, and all seems hopeless Ash apologizes for not being able to keep his promise, then sheds a tear before nearly dying. Victini then pulls off a Heroic Sacrifice, making it a Disney Death at the end of the movie.
An early novelization by one of the anime's major writers talks about Ash's father. They fell in love, married at age eighteen, and he ran off onto his journey. To top it all off her mother had just died and Delia was left with a restaurant and a newborn. He's been missing ever since and has achieved little to nothing. Ash's mother has exaggerated his father's legacy, not wanting to ruin Ash's perception of him. He was a mediocre trainer.
The same books say that being a gym leader is a terrible career. They are disqualified when they lose three times in a row, so they often bribe challengers to let them win. It costs a lot of money and the government doesn't give them enough. Brock's siblings have many fathers. They kept on running away and so Brock's mother had to marry again and again, having multiple kids. Eventually she ran away herself. Brock is so love-struck because he wants a woman to help take care of his family. The book states Misty's parents ran away but it doesn't give much info about them.
Note that these books are most likely no longer canon, as these details contradict many things in the anime proper.
Bianca's reaction to losing to Cameron in BW104. It was obvious how excited she was at being able to compete in the Unova League tournament, and to have all of that taken away from her so quickly... It really doesn't help that this is the first time we've ever seen her actually cry on-screen, not just have tears well up in her eyes, especially considering how upbeat and cheerful she is normally. Luckily she gets over it, but still...
In the Johto episode "Forest Grumps", Jessie (who is sleeping in a cave with Ash and Brock) remembers talking with a woman when she was a child, telling her she wanted to be a Trainer and a celebrity when she grew up. The woman tells little Jessie, "It sounds like you're going to have a very interesting life!" The sad part kicks in with Jessie's realization that her time on Team Rocket is miserable and not anything like what she dreamed.
Before this episode, Jessie met up with a Blissy she knew in school. It then goes to a flashback of her when she was even younger, and wanting to apply to become a Pokemon nurse. She did "not meet the requirements" to become a nurse. But you then see she did very well at taking care of the Pokemon, and it seems it's implied it was because she didn't look like a Nurse Joy.
In the Kanto episode "The Kangaskhan Kid", a mother and father search for their son Tommy who was lost at 3 years old, only to have Ash & co. find him at the Safari Zone living amongst the Kangaskhan a la Tarzan. Near the end of the episode, Tommy's parents help foil Team Rocket's plans via Heroic Sacrifice and afterwards, Tommy starts bawling his eyes out, thinking both of his parents are dead. It's revealed however that both of Tommy's parents survived the attack and tell Tommy that they will both live with Tommy and the Kangaskhan. The family is reunited once more.
Basically, anytime Tears, After the Cloudy Weather plays. You just know it's going to be one of those moments whenever it plays. To hear it in its entirety, go here.
The Espurr's backstory in "Seeking Shelter from the Storm!". It had been cared for by an old lady, but she fell ill and died. Espurr didn't realize she had passed away, and was waiting at her mansion so that it could show her its gratitude. Fortunately, the woman's granddaughter befriends it, tells it the truth, and offers it the chance to pay its respects at the woman's grave.
Magical Pokemon Journey gives us a singular example. In a series that's usually sunshine and rainbows, smack at the end of volume 7 we get a random story of a senile Quagsire looking for the Charmander he used to love. They find the hill where they promised to meet only to find her grave. She'd died three years before. Quagsire stands at the grave and sobs his tiny little eyes out, his memory fully returned. Her spirit shows up, and the two of them fade away. He's alive though—turns out what we'd seen was an astral projection. But when we see him again, all his memory is gone. It was for nothing. The ultimate kicker is that this is what Viz finished their run of the entire series with.
Pokémon Golden Boys has Black's Bayleef, later Gold's Bayleef. After its been released by the Jerk Ass that is Black, it takes quite a lot of time for it to get over Black's notion of it.
Pokémon Zensho has a small example in what happened to Shigeru's mom. All other adaptations tend to keep their "mysterious disappearance" ambiguous, but this manga makes it quite clear that they died in a car accident when their children were quite young. It makes even Shigeru look sympathetic to an extent, though the tears tend to be shed more on his sister.
On the same token, the redemption of the one responsible for this, simply through the protagonist Hareta's showing him compassion even when he has no reason to, may also bring out the waterworks. It's especially poignant because it is - so far, at least - the only storyline in which Cyrus is able to perform a Heel-Face Turn. For anyone who's a fan of Cyrus in normal canon, this is especially therapeutic.
Phantom Thief Pokémon 7 has Hiori's search for his long-lost sister, and the events after they meet. His sister, who has Identity Amnesia, has been taken by a terrorist group and created into a dangerous monster. He tries to snap sense into her, and she just beats him.
The ending for Grovyle's special episode in Sky. Oh. My. God. The Delayed Ripple Effect catches up with them as Primal Dialga is defeated, the world starts growing brighter as time begins moving again. Dusknoir vanishes while asking if his soul shined, and then Grovyle and Celebi watch the sunrise together as they too begin to vanish from history.
The ending to the game where your main Pokémon fades out of existence by restoring the timeline, and right before the credits, your partner breaks down and cries in front of Bidoof. This was so moving that even Dialga felt their pain, and brought your main Pokémon back into existence.
The music and the dialog makes this scene even harder to watch.
The ending to Igglybuff the Prodigy was definately a big one, too. Poor master Armaldo.
The resolution of the story between Gengar and Gardevoir in the first game.
Not a scene but rather a music piece (and fan-made, at that), but this remix of the Dark Cave from GSC/HGSS is just...ugh...
In Pokémon Mystery Dungeon, Kangaskhan's phrase upon reaching low health qualifies. "I'm done... Please, take care of my baby..."
Cyrus's backstory. Just... nngh. Especially when you find out that his grandfather KNEW he was going insane and almost intervened... but for some reason didn't.
According to the old man, Cyrus was an aloof but otherwise relatively normal child prodigy, who was slowly broken and then gradually turned insane as he was forced to live up to his parents' unreasonable expectations. Grandpa saw what was happening. Why didn't he save Cyrus? He didn't consider it proper to tell them how to raise their own child. Listening to that, and the regret he expresses as he tells his story, and especially knowing how twisted Cyrus ended up, and knowing that if the old man had intervened Cyrus could have grown up happy and adjusted...is heartbreaking.
It's even sadder if you're aware of the Real LifeValues Dissonancethat this story reflects: in Japanese culture, it is considered extremely improper to "butt in" with other families when you suspect that bad things are happening in that family - this causes many children to suffer from physical and/or psychological abuse from parents/friends/grandparents, such as what happened to Cyrus. His grandfather's regret is a Take That to the destructive social attitude of Pride, as well as the fear of social reprisal, that ruins children from a young age and leaves them messed up in later life - Cyrus represents that "worst case scenario" as the potential consequences of people not saying Screw the Rules, I'm Doing What's Right more. In addition, Cyrus' parents are the absolute expreme of the attitude in Japan that you must try your utter best no matter what - what was his best was never good enough for them, and coupled with his Ambiguous Disorder it's small wonder he was left damaged and nihilistic, when he could have grown up to be one of the greatest heroes the PKMN-world has ever seen... even without his intelligence, it's a massive waste because he wasn't predestined for evil (as opposed to someone who consciously ignored morality out of selfishness or a cruel streak), but the callousness of his parents ruined him.
In Pokémon FR/LG, in the Sevii Islands, there's a boy whose Onix died, and he is polishing a monument for it. It got me a bit more than it should have.
It turns into a Heartwarmer if you decide to leave a Lemonade on the monument, which was the Onix's favorite drink. The boy thanks you and gives you a TM for being so kind.
The ending for the sequel was much more heart-wrenching than the first (although that was sad, too) but what with the tearful, sudden goodbye bid to your partner before you cease existing, then your partner later breaking down on the beach (where they met you) and the credits rolling. Its such a sad ending, until Dialga brings you back.
The anime adaptation of the scene only makes it even more heart wrenching. "I'll leave it to you to protect... this world's beautiful mornings."
The true tear-jerking moment began when Grovyle said:"And Chimchar! You take good care of Piplup!" Chimchar: "But I can't do what you can do!" Grovyle: "You'll do just great!" He begins to fall towards the portal. "You two are a great team, and don't you ever forget it!". He falls into the portal. Right before he enters, he says: "The future of the world is in your hands. Protect the sunrise... for everyone's sake."
"I am, up to the very end, not wavering, honestly. I lived because of you Grovyle. Thanks to you I have no regrets."
Add to this the Igglybuff Special Episode on Explorers of Sky. You play the episode as Igglybuff, who makes a friend in Armaldo, a retired explorer. The two of them go exploring dungeons together, and the two grow to enjoy adventuring as a duo. Then the bomb gets dropped at the very end when it is revealed that Armaldo is actually a outlaw that has been avoiding capture for quite some time, and is arrested. Poor Igglybuff has to bear witness to all this, and Armaldo tells Igglybuff that he has had fun exploring with him. And when the day came that he was released, if he felt the same as he did now, he'd gladly explore with him again. He then gives Igglybuff the first treasure that the duo had found together, and is escorted away by Magnezone. Igglybuff breaks down crying for his friend as he's taken away...
"There are plenty of criminals out there... they are caught and punished, but... but... truly bad Pokémon... don't really exist anywhere." Cue horribly tear-jerking credits music!
Gates to Infinity also had those too... especially when the player character breaks down and cries.
Bonus points on the English version ending:
Player: (Sob... [Partner's name]... Even when you said... you wanted me to stay... Even though I promised you...)
Flashback appears. After it ends, it cuts back to the player.
Player: (But... You already knew, didn't you? That I... wouldn't be keeping that promise... That I would have to leave you someday. And... in the end... When our eyes seemed to meet across the sky...)
Player: (Those eyes... The way those eyes fixed on me...)
End of flashback.
Player: (I'm sure of it... [Partner's name]... everyone... You didn't forget about me. You remembered me, didn't you? You looked up at that light, knowing it was me... to say goodbye... You even managed to overcome your fate to forget me... [Partner's name] still... Everyone still... They still remember me... [Partner's name]... My... friends... Sob...)
The very first Pokémon generation, as well as their remakes, include the Lavender Town plot. The Lavender Town music is slow and kinda sad on its own, and its biggest feature is Pokémon Tower, a graveyard for departed Pokémon. That's not why the town's plot is so heartbreaking. Apparently, Team Rocket tried to capture a rare Cubone, but its mother saved it - and the Rockets killed her. You actually meet both the little Cubone and the vengeful spirit of mama Marowak... and it's up to the player to calm her spirit by facing her in battle. Mr. Fuji is praying alone for Marowak's spirit...
Pearl and Diamond manage to pull this off with one hell of a Player Punch as well. The main character arrives at Lake Verity too late, and Team Galactic has already set off a bomb in order to drain the lake and capture the Legendary Pokémon living in it. As a consequence of the explosion, you see Magikarp and Gyarados that were also in the lake, now flopping feebly on the dry lake bed in their death throes. A nearby Galactic Grunt just shrugs and states that those Pokémon are useless, so their mass slaughter is acceptable in order to Take Over the World.
While it's common knowledge now, fighting through a game that can take 120+ hours to beat and finding the first game's protagonist isolated and alone at the very end was a kick in the face.
The Fridge Horror sets in when you realize that he's been up there for a while, shutting himself off from the entire world, including his own mother, whose dialogue implies that she hasn't seen him at all in a very long while. The possible reasons for this behavior are awful in themselves, one of them being that, despite being 14 years old at most, he's done everything he set out to do and then some, and he never figured out the answer to the question, "and now what?"
Finding Cinnabar Island completely desolated in Gold and Silver. Surfing south from Pallet Town to go back to a favorite place from the first game...and it's gone. The saddest part is the story about Blaine, and how he's now all alone on the Seafoam Islands, no trainers, no gym, just him and what Pokémon he has left. Thank God he's at least got company and a renovated gym in the remakes.
Finding out, after you've beaten him and sent him into self-imposed exile, that Cyrus has a grandfather who cares deeply for him and blames himself for the boy's life winding up so terribly.
Silver screaming after Giovanni about how he'll be the strongest and never have to rely on anybody. The boy's only around seven or eight in that scene and just watched his failure of a father walk off on him.
Pretty much anything in the GS remakes where Celebi is involved. You just end up feeling sorry for both Silver and Team Rocket; the former was a sociopath because his dad was never there, and Team rocket's big takeover of the radio station is now all for naught. Neither of them will ever see the most important figure in their lives again. Worse, he doesn't even turn the radio off before the game suggests he's jumped...
Yamask, full stop. Just look at its PokéDex entries!
...unless you're playing the Japanese games, where it wasn't. Also for these who don't know what's going on - on February 1, 2003 the Space Shuttle Columbia was reentering Earth's atmosphere over Texas and Louisiana, only to disintegrate and kill all 7 members. This happened shortly before it was supposed to conclude its 28th mission.
It's implied that Maylene's father is a gambling addict who rarely ever leaves Celadon Game Corner. Maylene doesn't look that much older than the eleven year old protagonist, and she's implied to be rather poor.
In Pokémon Conquest the whole game might be one when you consider that everyone in the game actually gets along compared to their real life counterparts, so when their profile says that they are loyal to their master until the very end, you look at history and want to cry.
Speaking of Pokémon Conquest, Hanbei's ending comes off as this along with a Fridge Horror. In the game, Hanbei is portrayed as a young boy. In real life, Hanbei died of tuberculosis during an important battle that Hideyoshi instigated to another nation. In the game, after he wins the junior battle, he starts coughing uncontrollably. Hideyoshi asks if he's sick and Hanbei just replied he got too excited. Kanbei looks at him and Hanbei glares at him telling him "Don't say anything" before switching the subject. It's very obvious that the ending implies that Hanbei probably died shortly after the whole battle and what's made worse is that unlike his real life counterpart who died in his mid thirties, Hanbei is at least a teenager and would probably die even younger than his real life counterpart.
The credits of Generation III. The music is part of it, but what really kicks you in the face, especially when you come back to your original save file that's been around for almost ten years now, is that last picture. All through the credits, it cycles through all of the Pokemon you've captured over the years, and then, the very last one, it shows a picture of your original starter. Maybe it's just this troper, but it brought back memories of me as a kid, fighting that first battle with May, it evolving, etc.
Nuzlocke challenges — for the uninitiated, these are a fan-made alternate playstyle where the player has to release any pokemon they have that faints in battle, as battles in the setting are purposefully retconned as being fights to the death and, thusly, a player's pokemon that is knocked out has to be treated as being killed. They may be a Self-Imposed Challenge, but it's still a real gut-puncher when you see what happens when you take such a Darker and Edgier stance on the setting. Particularly when a Pokémon you have raised since the beginning dies or your favorite dies.
Alternatively, they're upsetting for a different reason. To some players who grew up on Pokémon, Nuzlockes are a serious Player Punch due to the inability to accept the idea that Pokémon beaten in battle die (the constant reminders the game gives that they're just fainted only reinforce that). As a result, it paints the player character as obsessed with winning to the point of abandoning any Pokémon that can't win a battle; the mere idea of someone who began the game young and innocent becoming so corrupted by obsession is.... upsetting, to say the least.
Come Generation VI, and Nuzlocke runners now have another unenviable choice: using Pokémin-Amie to bond with their team gives them a critical chance to survival otherwise fatal blows, with The Power of Love no less, but imagine how much more the loss will hurt after you'd fed them, patted them, played games together...
Want to add even more poignancy to the Gen III end-credits? Play a Generation III Nuzlocke Challenge, and it gives the images a lot more power and context considering what happened to some of those mons.
In Pokemon X and Y, probably the biggest tearjerker in the entire game was the story of a general in a war 3000 years ago. He was best buddies with his Floette and they did everything together, but in said war his Floette died. He was ultimately heartbroken, so he created a device to bring his Floette back to life, but in doing so he had to sacrifice the lives of other living Pokemon. When his Floette was revived, and found out what he did to bring it back, it was beyond repulsed and ran away. The device had also made Floette and it's trainer both immortal. So the man traveled the world ever since, looking for his friend to beg for forgiveness...
And then it was revealed that he was alive all along... for 3000 years. So he's been Walking the Earth for that long, atoning for what he has done. Then he gets kidnapped and imprisoned by the person who wants to use the device he built, the very same device that caused him his eternal punishment. Imagine the heartbreak and sadness he feels thinking of that single incident that robbed him of his best friend. Granted, it ended in a Crowning Moment of Heartwarming, though.
Maré Odomo's Letters To An Absent Father is a series of strips in which the framing device are letters sent by Ash to his father. For those who played Gold/Sylver/Crystal/HeartGold/SoulSilver all the way to the end this one◊ is a downer in many levels.
Not quite! One last strip◊ has been added and it's much more hopeful but still very much a Tear Jerker, just for a different reason.
This story◊ about what one player's shiny Absol means to him.