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Tear Jerker: Yu-Gi-Oh!
During their duel with Pegasus, Yugi collapses before he and Yami can pull off their mind shuffle.
Yami: Yugi? Yugi! I can't sense his spirit. I can no longer feel the presence of his young mind. (voice breaking) No! He...he can't be gone!
Bonus points for it being the first time anything like that ever happening to poor Yugi... though not the last.
Extra points for it being the first time we get to see Yami so heartbroken... though it wont be the last time we see that either.
The duel between Yugi and Marik-possessed Joey:
Specifically when Yugi smiles and tells the now dispossessed Joey what happened with tears rolling down his face, then Joey starts screaming in panic when he realizes Yugi has pretty much set himself up for death...
"Joey...You're my best friend..." Both the anime and the manga (which survived in Viz's English print) had this in (though the 4Kids dub removes the line, perhaps due to its context), and sets it up for Yugi's final move of the duel.
Also right after that in the manga: Tea, Tristan, and Serenity catch up to Yugi and Joey right after the incident, with Joey, rather than being happy to see his sister, being deeply ashamed of himself that he almost killed his best friend. After Mai attempts to slap him out of it (no pun intended), Serenity takes off her bandages after explaining how Mai told her about everything Joey did for her in Duelist Kingdom, and finally getting the courage to open her eyes and her vision gradually fades in to see Joey.
At end of the series, Atem finally goes to the afterlife and says goodbye to Yugi & co.
Then there's the episode in which Jonouchi brings himself out of a coma just to go watch Yugi dueling. Especially when Honda had him by the neck and was shaking him, telling him he had to wake up because Yugi -their Yugi- was fighting, and Jonouchi had to be there.
What about when Yugi chose to let himself be taken by the soul-stealing Seal of the Orichalcos instead of Atem? The fact that Atem himself breaks down into tears and poor Anzu telling him "Pharaoh, please... he's gone..." just makes it worse and worse. *sniff*
It gets worse when Atem later battles against Yugi's imprisoned soul in a cursed area -with Yugi yelling accusations at him and turning Yami's earlier, heartless tactics against him, proving that yes, he does, actually, have a mean bone in his body. Turns out it was being cruel to be kind as only by seeing the depth of his errors and defeating Yugi could Yami finally move on. Then seeing Yami run to him and cradle him in his arms, with Yugi still smiling, even as he vanishes for a second time, opens the floodgates.
Towards the end of the duel against Dartz, Yami is facing down a seemingly indestructible monster. Dartz tried to convince him to surrender, and almost succeeded. Right when the Orichalcos encircles him, Yami sheds a tear, and gives the best friendship speech and "It's my turn! I draw!" line in the franchise.
Mai, coming out of her brain controlled craze just in time to run across the arena and catch a defeated Jonouchi in her arms, and realise what she's done.
The saddest scenes involved Marik's back-story (much of which was cut from the dubbed version): Odion/Rishid approaching an injured Marik with intent to kill him, only to have Marik refer to him as his brother, causing Rishid to drop the knife and burst into tears; seeing young Marik dragged off in front of Rishid for the carving ritual while poor Rishid can only stand by; then seeing Marik's horrified reaction after he discovers that he killed his own father under the influence of his "dark" side.
Okay, Noah's arc was one of the most inconvenient fillers ever, it's true. But wow, is the ending sad! Noah finds out that his father is also in the Virtual World, and is happy to see that his dad really loves him. But reality crushes him when his father says he was a disappointment and basically called him useless. Mokuba sees this and shows pity for his never known foster brother (even though said brother Mind Raped him for most of the season). At first Noah tries to get advantage of this to use Mokuba's body and escape to the real world; but in the middle of the plan he notices that he really does love his "brother" Mokuba and doesn't want him to die. He then gives Mokuba his body back, says goodbye and stays with his father in the Virtual World while it is destroyed. And in the end of the whole thing, Mokuba gives his brother a quick funeral, while Noah's voiceover goes saying that he is not a machine, but a human. Why did the dub cut this...?
There's a scene in episode 52 which at the time seems little more than fuel for yaoi fangirls, but in retrospect, after seeing the final episode, Atem saying that he wants to be with Yugi forever, and Yugi offering to give Atem all his own memories in exchange for the ones he lost, becomes a bit of a Tear Jerker, because you know Atem can't stay, and how this is all going to end up.
The episode before also contains a big one. The Puzzle has been stolen, chained to a wall, and broken into pieces and now the whole building is on fire. Yugi refuses to abandon Yami and the Puzzle and stays in the burning building to complete the Puzzle and try to free it from the chains. Even when he passes out he still protectively clutches the Puzzle and refuses to let go.
Anzu's duel against Mai, especially when she knows damned well she doesn't have a hope in hell of beating her always makes her tear up.
Kisara and the priest in the last season. It gave a lot more meaning to Seto's actions.
ITA. These scenes were particularly heartbreaking because - despite their obvious feelings - Kisara and Seto get barely five minutes to talk before she dies.
Pegasus' back-story is rather depressing, especially in the manga. He lost the love of his life that was presumably his only friend at the same time. Looking at him curled up, sitting in a fetal position among the paintings of Cynthia with a blank face is totally gut-wrenching. He even mentions he "stared at the blank canvas of his heart". He goes to Egypt in order to reunite with her in some way, but he only gets to witness a poor man getting burned to death by an ancient artifact in front of his eyes. And that's right before his turn, he even begs Shadi to let him go. The latter convinces him he'd meet his love again if the Eye accepted him. Thinking this is his chance (not that he had much of a choice in the matter), he has his left eye replaced for the Eye. He gets to meet Cynthia, but only for a fleeting moment. He reaches out for her while having tears and blood rolling down his cheek, but then she disappears, leaving him one eye less and with all his pain, breaking him even more. Even Yugi's friends felt sorry for what the man went through. And then she realized why Pegasus kept referring to the Toon Monsters as "perfect life form" and how they can never die. The death of his beloved hit him so hard he actually stepped back into childhood and denied death. After telling Yugi his back-story, one may think he finally redeemed and was let go from receiving the Penalty Game from Yugi... But then Dark Bakura steals his Millennium Eye while mocking him by leaving a replica of it behind, leaving Pegasus to die, but allowing him to reunite with Cynthia again. Although it is assumed he moved on and accepted her death.
In GX, their are a few times that show he's gotten a little better for the experience.
During the memory world arc, seeing Thief King Bakura's past is insanely sad. When it show the entire massacre, and then the small child Bakura hiding and seeing it all. And then later on, when he is turned to sand, and is shown to be nothing more than a pawn for Yami no Bakura's game.
It gets worse when, after wondering how on Earth the spirit of the Ring could have someone as kind and gentle as Ryou as a reincarnation/destined vessel/half of a soul, you realize that it's because Bakura was the same, at least until tragedy struck and marked him forever.
This one is probably not quite a Tear Jerker, but more a case of... Fridge Sadness? Anyways, in the anime, Seto had quite a prominent role, even after the Battle City Arc. He was present during the Memories Arc, and during the final duel between Atemu and Yugi. However, in the manga, wasn't present during the final duel. On the penultimate page, though, he had arrived. Given that Seto is not as skeptical as the dub wants to make you believe, it is probably quite reasonable to assume that he arrived to witness the final duel and maybe even say good-bye. But he was too late, and probably just saw the tomb collapsing.
The talk Yugi and Atem have on the school roof in episode 199, about how Yugi's stronger now and he'll be fine if Atem leaves, so Atem shouldn't hold back. Just Yugi's total selflessness and willingness to do whatever it takes to make his best friend happy, even if it means he can't see him anymore. It also shows how far Yugi's come; at the beginning of the series, he'd be crying and begging Atem to stay. Just... just... ;_;
In the same bit, you have the conclusion to the Yami/Anzu/Yugi love triangle sub-plot: Tea goes to Yugi's room so she can have one last talk with Yami, and it's obvious that she's intending to confess her love to Yami before the duel that decides whether he stays in the modern world or goes to the after-life. She asks Yugi if he's heard Yami say anything, and she's about to ask him if he can make the Other Yugi come out...but she ends up not being able to do it and leaves the room, having given up her last chance to tell him. Just after she leaves, you see Yugi think to himself "I know how you feel about him, Tea...", so he knows EXACTLY what she wanted to do...but despite that, he's not jealous because he wants her to be happy. SOB.
Before the card game was the focus, there were a ton of different games, one of them was a tamagotchi thing, we saw Yugi saying good-bye to his at the end of that story, and dammit, it's just depressing.
In the Waking the Dragons Arc, Raphael is quite a sympathetic character. Look at this: He loses all of his family in a shipwreck, and lives ten years alone on an island with Duel Monsters for company. He returns and there's a big hulabaloo about his return but he's not happy. Then, when he meets with Dartz he's forced to dig up the graves of his siblings and his Guardian Eatos turns evil. Then when we get to his second duel with Yami, he sees visions of his family saying that they'll always be together and he's actually smiling for the first time in years. Then we find out that Dartz intentionally did this, and caused the storm that killed his family. Please give this guy a hug...
The part in Yami's first duel with Raphael when Yami, under the influence of the Orichalcos, starts sacrificing his monsters left and right in a reckless attempt to win. Dark Magician Girl becomes terrified and actually begs Yami not to kill her, but he does it anyway.
That entire duel is a huge Tear Jerker. First we have Yugi breaking down, frantically begging Yami not to play the Seal of the Orichalcos, grabbing his arm and reminding him of the promise they made. When Yami plays it anyway Yugi's despairing "Nooo!" just before he's locked away is heart-wrenching. He spends the rest of the duel trying to reach Yami.
Then Yami, loses the duel thanks to his own short-sighted pride and cruelty towards his monsters (which are at the time, real), while the Seal of Orichalcos is on the field. This means that Yami's soul must be taken as per the Seal's rules. At the last second, Yugi breaks through the seal that had been separating them and gives up his soul instead, saving Yami. That's depressing enough, but just as painful is Yami's My God, What Have I Done? moment when he realizes what has happened. He spends the next few episodes in a Heroic B So D and even when he snaps out of it he's shown to be constantly replaying the moment in his head for the rest of the arc.
As much of a Jerkass Kaiba can be sometimes, seeing him during the latter part of his duel with Noah can make you pity the guy. Right before Kaiba can pull off a win, Noah uses the possessed Mokuba as a human shield. Kaiba can't bring himself to attack, and chooses the safety of his little brother over a sure victory. Later, Noah is whaling on Kaiba, who is close to tears trying to snap Mokuba out of his trance. Mokuba does break free, but Noah manages to beat Kaiba anyways. He gloats by turning the two brothers into stone. All they were trying to do at the time was be in each others arms.
Yami and Kaiba's duel against Dartz "Mirror Knights".
The part in the final battle of Battle City where a part of Malik/Marik's soul appears by the side of an unconscious Rishid/Odion. Malik fully expects that it'll be the last time he can say anything to Rishid, because his own soul will disappear if Dark Malik is defeated. He recalls that Rishid had been always loyal to Malik, sharing the pain and making a choice to live in darkness with him. Then Malik tells Rishid that he doesn't have to suffer anymore, he wants him to head towards the light, and thanks him before disappearing.
Kaiba's Heroic BSOD when he begins losing his duel to Yami Yugi in Duelist Kingdom and imagines Mokuba being eaten away inside his decaying Blue Eyes Ultimate Dragon while he can just helplessly watch.
Yu-Gi-Oh! GX, when Zane dies. Especially when Jaden promises that he'll "shine even brighter and make a miracle", and Zane says "I'm sure... everyone who died... wanted that too". And then with Syrus's sobbing going on and on...
Jaden's reconciliation with Yubel at the end of Season 3. After laying everything bare in a Motive Rant, the gut-wrenching embrace they have at the end isn't that far-fetched, really.
When Hassleberry, Alexis and Atticus die. The worst part isn't the deaths, it's the look on Jaden's face when they die.
What? No mention of Tear Jerkers from other seasons? Well, for starters, there's the ending to episode 30. Jaden has beaten Darkness and saved Syrus and Chumley from being killed in the volcano. Darkness was revealed to be Atticus, and Alexis was in tears when she found out.
And another first season Tear Jerker: Zane's sacrifice to save Syrus from Camilla, as a slow, tinkly music box version of Genkai Battle plays in the background.
The end of Episode 39 in Yu-Gi-Oh! 5Ds. Basically, Carly has come Back from the Dead as a Dark Signer and avenges her own death by killing Sayer and, by being undead, cannot return to her normal life. Once sherealizes this, she is, needless to say, overwhelmed.
The end of Episode 46 is also pretty sad.
The tragic conclusion of Episode 59 - everyone knew this was going to happen eventually, but it didn't change how sad it was when it finally came, especially since it recalls the similar Tear Jerker with Mai and Jonouchi during Waking the Dragons, except with the roles reversed.
The end of episode 64, especially due to the lead up. Not because it's sad or anything, but it's because ''All their hard work paid off. The Dark Signers (Sans Godwin and Roman) were resurrected, and the Daedalus bridge was finally finished.
Yusei (smiling): Riding Duel, ACCELERATION!
When watching the few scenes where Yusei cries over something, particularly in episode 57, where after confessing the guilt he feels over his father's research ruining his friends' lives, he demands an answer from Roman about how he's supposed to redeem himself. Crow does make it rather Heartwarming when he answers Yusei's question instead, though.
Akiza Izinski's backstory is one of the most heartbreaking parts of the series. After being teary-eyed for the better part of the entire episode, watching Sayer hug Akiza and realizing how much he really meant to her was what finally elevated this scene to the burst-out-in-tears level. Especially after Yusei wakes her up and she asks, "Yusei... You came to save me?" Yes, the ending where she wakes up and realizes Sayer is dead (or so she thinks) is absolute Narm, but it was so painful getting there. And to be fair, after seeing her parents for the first time in years and just barely surviving a death duel, her reaction was pretty justified.
Crow dueling the old man Tetsuzo in episode 68 gets pretty gloomy. Jack and Yusei wonder why the old man isn't pulling out a sure-win combo of combining the Kid Junk monster with the Maternal Junk and Paternal Junk monsters already on the field. It turns out that he doesn't have that card at all, because his beloved son has it and his wife took him away when she left him years ago, which is why Tetsuzo is so attached to his home, which is now in the middle of a junkyard.
Hey, don't forget Yusei's dad putting him inside the escape pod, then dying after words.
Aporia and ZONE's fates, essentially Aporia lost his parents, his girlfriend and was one of the few humans left that survived the apocalypse. But even when he and his friends tried to experiment to come up with a solution, all of them died of old age including himself... except ZONE. ZONE was left alone and was force to use his friends in order to create robots and travel to the past to set things right.
Bruno and Aporia's deaths.
When Jack, Leo, and Luna's duel with Aporia. After his Heroic Sacrifice to protect his sister, Leo doesn't just drop to his knees in defeat...he falls flat on his face with a soul-crushing thud that drives the point home: He's not just defeated, he's dead. It especially hit true with Luna, whose own heartbreak at the loss of her brother was, as indicated by the slow roll-down of her Life Points, about to kill her as well.
ZONE taking Yusei's place to fully reverse the Ark Cradle's generator. Yusei screaming his name is absolutely heart-wrenching.
Episodes 46-49. III's absolutely breaking/broken from how much his family has changed.
Episodes 57-58. Pretty much the above, except applying to IV now. And to add to this, Tron brutally does not give a shit about IV's feelings, even helping his opponent, Shark win.
Episode 67: After acting absolutely inhumane for half of the series, Tron willingly lets himself get sucked into the Sphere Field, giving back all the souls that he took in the process...including the souls of his sons, finally showing that he does care about them in the end.
Episode 111: Astral dies trying to defend Yuma from Number 96's attack, taking the blow himself, and having to withstand the corruption. Yuma and Kotori are utterly in tears, and Shark and Kaito are also saddened terribly.
Pretty much the entirety of Arc 6 (Episode 124 and on). Most of the supporting cast dies, along with the Arclight brothers. Shark and Rio, having now become Nasch and Merag, are trying to play themselves as cold and ruthless, but cannot do so. Don Thousand's meddling with the lives of Alito and presumably the other Barian Emperors is revealed, and Vector tries to take the rest of the Emperors out. And, of course, Durbe dies.