Turns into a heartwarming moment when Chazz breaks free from the mind control and uses his Ojamas again.
Chazz, Alexis, Hassleberry and Atticus all being sacrificed by Brron and seemingly killed off. Along with Jaden watching in horror.
Jaden trapped in the mind of the Supreme King. The happy-go-lucky hero who's reaction to immensely powerful harbingers of doom and darkness have ranged from comedic to inspirational is trapped in a perpetual Despair Event Horizon where he's unaware of the horrible things the Supreme King is using his body to do, and where he can only wallow in self-loathing as he blames himself for his friends' apparent deaths.
Also, the build-up to said breakdown. It was really apparent that Jesse's loss in the first dimension took its toll on Jaden, and each dimension saw Jaden get more reckless, just wanting to find his friend. The new 'death with a loss in a duel' made things harder, because then duels weren't even fun anymore. Jaden had to keep fighting, and by the time he faces Brron, he reaches his limit when his friends are sacrificed, putting on a stoic front for the sake of not breaking down. It was only with Syrus calling him out on his recklessness that he finally snaps.
The above entry is so traumatic for him that he spends almost the entirety of the final season as a cynical Hurting Hero. He rarely spends time with his friends, almost never smiles, only duels—his passion and most joy-inducing pastime—when doing so is absolutely necessary when it comes to saving the world.
His duel against Syrus in season 2 gets even more heartbreaking when you realize that Syrus only kept hold of his ideals because Jaden was there to support him. If Zane had had one single person who still believed in him by the time he ended up in the Underground, he might not have broken.
His death scene somehow takes it even further, especially when Jaden promises that he'll "shine even brighter and make a miracle", and Zane responds, "I'm sure... everyone who died... wanted that too". In the dub, Jaden futilely tells him to hold on, saying that Syrus needs his big brother, and Zane replies that "he's got one" before telling Syrus that he's proud of him. Add that to the images of him that appear in the sky (Hell Kaiser, then him at Duel Academy, and finally him as a child), and Syrus's sobbing going on and on...
He only appears in two episodes of Season 4, but it's painful to watch him in his condition. His heart condition has finally caught up with him, and even the powerful will that let him fight through it last season can't keep him on his feet. Not to mention the reveal later in the season that his brother apparently resents the living hell out of him for needing a caretaker.
Syrus in season 3. After losing his big brother emotionally, he now faces the same situation with his best friend. By the end of Season 3, the viewer clearly sees Syrus in tears, wanting Jaden back after everything that went down. He clearly regrets how he treated Jaden and his mere expression at the thought of Jaden sacrificing himself in Episode 155 was heart wrenching. The fact that the Japanese version had Syrus revert to his original "ANIKI!" (especially after a few dozen episodes of his calling Jaden merely by name with a monotone voice) when emotionally calling out to Jaden sold it. Thankfully, it turned Heartwarming when Jaden eventually returned, but with Season 4 and Jaden's distance, their relationship will never be the same again.
The scene after Zane rescues Syrus from Devil Dozer is a mix of heartwarming and tearjerking. Their relationship is obviously (and forgoodreason) strained and Zane is incapable of being nice, but he does encourage Syrus to watch over Jaden if the friendship is still important to him. In his own socially-inept way. On the tear-jerking side, Zane asks why Syrus was willing to stand up to him last year, but not to Jaden now... and then says, "Maybe you're better off without him. Just like you're better off without me." Zane knows he's dying. One last time, he's trying to protect his brother from how much of a wreck his own life is.
Jim trying to save Jaden from the Supreme King. Jim knows Jaden is Not Himself and desperately tries to reach Jaden inside. Why? Because Jaden was his honest and simple friend. Despite Jim's Determinator attempts and a fierce duel, the Supreme King cruelly kills Jim without any remorse.
The flashback of a young Yusuke Fujiwara losing his parents at the morgue and Honest appearing to embrace him.
The end of Hassleberry and Professor Satyr's duel is this and a heartwarming moment, when Hassleberry figures out that he pulled the scheme to pull the Ra's at the Red Dorm back out of loneliness, because he didn't want to be alone in the dorm anymore.
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.
Professor Viper's backstory is heartbreaking, despite how he had been, you feel for him when his adopted son dies. And then Yubel lied about resurrecting him. The Japanese version just twisted the nail further into the coffin when Yubel changes Viper's memories so that he thinks his son is still alive, walking off the tall platform everyone is standing on to his own death. Viper's death is still one of the darkest moments the franchise has had when ending a duel.
From Season 4, Episode 178: Yubel being forced to attack Juudai head-on by Darkness. The look on her face as she's forcibly dragged across the arena an inch at a time is absolutely heartbreaking. Followed by a Crowning Moment of Heartwarming when Juudai takes her hand and vows "I'll get you back, no matter what!"
Fubuki screaming for Asuka after she's lost to Darkness.
From the manga, when Midori realizes she has to sacrifice the possibility of getting information on her younger brother Koyo's coma out of Reggie to prevent Judai from having to duel her, accompanied by a mental vision of Koyo telling her she's doing the right thing. She's unable to win, though, and collapses, comatose in front of Judai.