* Aster's memory of the night he found his father murdered. He picks up the Destiny Hero Dreadmaster card realizing those cards are all he has left of his father while crying.
* 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 DespairEventHorizon where he's unaware of [[spoiler: the horrible things the Supreme King is using his body to do]], and where [[spoiler:he can only wallow in self-loathing as he blames himself for his friends' apparent deaths.]]
* The above entry is so traumatic for him that he spends almost the entirety of the final season as a cynical HurtingHero. 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.
* The other BrokenAce, Ryou/Zane, was just as heartbreaking. Used to be respectful despite his stoic and aloof behavior, he finally [[FreakOut snapped]] after a humiliating loss and [[BloodKnight willing to do anything]] to [[SeriousBusiness achieve victory]] even at the expense of [[KickTheDog his little brother]]. Syrus is left heartbroken that he couldn't save his big brother. [[spoiler: Ryo gets better, but it's still sad to see the once respectable Kaiser bounded to a chair.]]
* Syrus in season 3. After losing his big brother emotionally, he now faces the same situation with his best friend.
* Jim [[IKnowYoureInThereSomewhereFight trying to save]] Jaden from the [[SuperPoweredEvilSide Supreme King]]. Jim knows Jaden is NotHimself 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.
* In season 3, [[JerkWithAHeartOfGold Aster is the only person concerned about getting the rest of the group to Duel Academy safely.]] When Adrian shows up, [[TheDulcineaEffect Aster refuses to allow Echo to be forced against her will as a sacrifice]] and challenges Adrian in a duel to the death. During their duel, [[UnwantedRescue Echo confesses she knows what she's doing for Adrian and doesn't want to be rescued because everything is for the best so Adrian can be king.]] Adrian is able to defeat Aster with Exodia and Aster is only able to say farewell to Jaden before the group was involved in the blast as he is defeated.
* Zane dying in season 3. He comes back in season 4 though.
* The flashback of a young Yusuke Fujiwara losing his parents at the morgue and Honest appearing to embrace him.
* [[IKnowYoureInThereSomewhereFight In Jaden's duel to save]] [[BrainwashedAndCrazy Chazz from the Society of Light]], Ojama Yellow, beaten and bruised from repeated attacks, breaks down into tears.
** Turns into a heartwarming moment when Chazz breaks free from the mind control and uses his Ojamas again.
* The end of Hassleberry and Professor Satyr's duel is this and a heartwarming moment, when Hasslberry 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.