* 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.