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Tear Jerker: Pokémon Mystery Dungeon
Red and Blue Rescue Team
The ending of Red/Blue Rescue Team had its sad notes, though not as bad as the following games.
The Red/Blue Rescue Team ending had other characters besides just the partner getting upset at the hero leaving. It's a bit jarring to see Team ACT, who had been willing to hunt you down, getting sad over your disappearance.
The scene where you have to flee town after Gengar claims you're the human from the Ninetales legend may not be as sad as some of the Explorers scenes, but it still manages to be pretty touching. It's mainly because of how Caterpie, Diglett, and Jumpluff all show up to see you off and tell you that they still believe in you.
A small one set after the ending of Red/Blue: You come back after disappearing, and your partner is so overjoyed to see you...and then a very short while later they basically tell you to stop hogging the position of leader and leaves for their friend area, never to talk to you again except for scripted events.
Explorers of Time, Darkness, and Sky
The pre-credits ending. All of it.
Specifically, The player was really sent back from the future to change the past, knowing full well that saving the world would cause him to vanish from existence. You only learn of this right before Grovyle throws Dusknoir and himself back into the future to prevent Dusknoir from interfering with your task of saving the world. You progress through The Very Definitely Final Dungeon knowing that the player can't reveal his ultimate fate to his most trusted partner, and after saving the world, has only enough time to give his final goodbyes before disappearing into the light and leaving his partner crying from the shock. Out of three Pokémon who left for the Hidden Land, only one returned to tell everyone about it, and it wasn't you. And that's not counting the Really Dead Montage when the partner recalls his memories of their adventures, and breaks down crying again.
The fact that this was basically the first time we see ourselves talk to our partner. Hearing the good-bye coming straight from the player just made it even sadder.
You: *starts to glow brighter* '...! The light...The light is getting brighter...'
Partner: "D-Don't! Don't...Don't go..."
You: "Thank you for everything, [Partner]. I'm glad we got to train together at the guild...I'm glad we got to go on adventures together...I'm glad...I got to know you [Partner]. "
You: "I'm sorry. I'm so lucky that you were my friend..."
Partner: "I feel the same way! To me, you're...more important than anything..."
You: "Yes...I feel the same way. [Partner]...Even after I disappear from here...I will never forget you... *glows brighter and disappears...*"
This music right before the credits of the Explorers games.
The end of Special Episode 2, "Igglybuff The Prodigy". Poor little guy has to watch his exploring master get arrested, not knowing until now Armaldo was a criminal.
Not to mention when Armaldo stopped Igglybuff from attacking Nidoking and Magnezone and then later giving him his Defend Globe before being carried away as Igglybuff cries his eyes out.
After returning from the Miracle Sea, Chatot makes you give up baby Manaphy for its own health and safety, leading to a painful separation.
Especially when Manaphy realises that he has to leave and has to be dragged away by Walrein, screaming your and your partner's names.
The end of Special Episode 5, "In The Future of Darkness". When the flow of time in the future is finally starting to resume, the eternal darkness is finally giving way to a sunrise ... but this also means that since the past is changed, this future will cease to exist any moment. Grovyle, Celebi, and Dusknoir have to fight to stop Primal Dialga from escaping the future, even though they will all soon be erased. Dialga first, Dusknoir second, Grovyle embraces Celebi as they watch the sun rise, with Celebi describing just how beautiful it is to finally see the sun again as the two of them (and everything else) vanishes.
Dusknoir vanishing was especially touching because after spending most of the game hating Grovyle, he thanks him for showing him what it means to live, and that he now has no regrets... *sniffle*
The beginning of Bidoof's Special Episode, with him saying goodbye to his family while sad music plays.
Bidoof's Mama: If you need us, you can always come home.
In that same episode, realizing that Snover and Team Rogue were a bunch of bad guys and they were about to take Bidoof's money from him.
Team Skull's last scene, Chatot's sacrifice and the scene with Wigglytuff afterwards and of course, Grovyle's sacrifice.
The anime version of Grovyle's sacrifice was just as heart-breaking as the game version, if not more.
When Fake!Cresselia comes and tells you and your partner that you're destroying the world and need to be killed (or kill yourselves) to save it. This can really hit home for those who have felt suicidal in the past.
Gates to Infinity
The death of Hydreigon. Even though he comes back at the very end.
It can also be sad to see your partner's reaction when Kyurem nearly kills you in a No-Holds-Barred Beatdown, with your partner unable to do anything about it.
The Reveal of what the golden orbs the townspeople see are. They're humans that came to the Pokemon world and failed in their mission to save it.
Unlike previous installments, you don't come back post-credits...until you play as the partner to work to bring you back.
Only halfway true, as the first post credits side quest involves bringing your character back for a joyful reunion... unless of course, you choose not to return. One can only wonder how your partner would feel after that...
Munna'sMotive Rant concerning their Start of Darkness. All she wanted was to be accepted and to have friends, and all she got was heartbreak and betrayal. Is it any wonder she bought into the Bittercold's promises of a "new, better world"?
Finding out that your partner is an orphan, and has been alone for as long as they can remember, at least until you showed up.
The part before the credits roll when the player breaks down crying. In the English version, the player starts sobbing after hearing the message in the Frism. The dialogue is as follows after the message:
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...)
In the post-game, whenever the partner wakes up and sees the empty patch of hay where the player character would have been sleeping at, every single morning.
Especially as it's pretty strongly implied that your partner is suffering from depression. The fact that he resolutely becomes a Stepford Smiler does not help at all.