The final battle with Red in Generation 2 (And its remakes) is uncharacteristically poignant for the series. No words, not even a flashy departure. When you beat him, his whiting out and scurrying off to the nearest Pokémon Center will bring tears to your eyes.
In a rarely-noticed bit of Fridge Horror, the realization regarding your rival in Pokemon Red And Blue. You see him in the Pokémon Tower in Lavender Town, and he asks you if you're there visiting a dead Pokémon. Last time you fought him, he had his Raticate, which you likely swiftly defeated and which he no longer has in his party. Now, this isn't to say that you're necessarily to blame...but keep in mind this is Red/Blue.
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 definitely a big one, too. Poor master Armaldo.
The resolution of the story between Gengar and Gardevoir in the first game.
The end credits for the second gen games do the trick for this troper.
Oh Jesus. The music box-style theme at the very end never fails to break this troper down. Also a CMOH at the end of the HG/SS credits when your character is shown running across the screen to your mom before the screen fades to black and the music box starts playing.
Thirded. Normally, I skip credits where I can, but these were excellent, especially when the backgrounds switch to clouds and you walk up to Lance, and then the part with your mom. The last section of the normal credit music is also surprisingly tearjerker-y.
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, why must you make me cry in the middle of the night...?
In Pokemon 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.
In Pokémon FR/LG, in the Sevii Islands, there's a boy who's Onix died, and he is polishing a monument for it. It got me a bit more than it should have.
How has no one mentioned the Marowak scene in the Lavender Town Tower in Red and Blue? This troper gets choked up just thinking about it. ;_;
The endings of both of Pokémon Mystery Dungeon generations. If you don't tear up at least a little, you're probably lacking a bit in the soul department.
This troper reached the ending of the first one and didn't feel especially sad, but he'd spent the whole game trying to return to the human world, which never happened.
When I reached the ending of the first PMD I cried so very hard, especially the part where your partner is crying after saying goodbye...
Personally, 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.
This troper is usually one to sit through sad moments of games without showing too much emotion (though there have been a good few that have got me), but the ending to that... I was actually struggling to hold back tears, cause I had completed it during a car journey home. I had to close the DS until I got indoors to my room to continue it. And it got me even worse, considering that I had named my Treecko partner after my best friend, who is a Treecko fan. The ending combined with the thought of losing my best friend... Thank God for Dialga reviving the character, as that would have been too much for me if he hadn't done.
Nightmare Fuel nothing. That was sad. Heck, for quite a while afterwards, even the music from that scene was enough to make This Troper tear up.
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... God, this troper got teary eyed just writing that all up...
"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! :D This Troper still cries playing that episode.
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. This troper was fully aware of just exactly how useless Magikarps are in battle and still was ready to reach through the screen and personally choke a bitch in a fit of Berserker Tears.
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.
For this troper, it was finding Cinnabar Island completely desolated in Gold and Silver. This troper was so excited, surfing south from Pallet Town to go back to his 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.