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Nightmarefuel: Metal Fight Beyblade
Metal Fusion/Metal Fight
Kyoya's defeat by Ryuga. Having a spear of dark energy impaled through your chest is NOT pretty!
Adding onto this, the dark power, itself. It continuously gained more and more power inside of Ryuga's body until it completely took control of Ryuga's body and made him take on the appearance of demonic, dragon-like creature.
Reiji. Let's do a list, shall we? He enjoys tormenting his opponents, even after he's clearly already won the battle (during his battle with Hyoma, for example, where we see Poison Serpent actually wrapping itself around Hyoma's neck in a way that would make someone think of strangulation), he has no qualms about scaring the everloving crap out of little kids and he talks like snake going after his prey. His eyes are also usually hidden and, when they open, he looks outright insane!
Yu being betrayed by Dark Nebula. The kid only lost one time and he was forced to battle Reiji, who stuck to his usual routine of tormenting his opponent. Made even worse when Yu spotted Ryuga watching him and crying out for his help, only for Ryuga to turn and walk away from him, showing that the person he thought was a good friend was only using him, shredding the last bit of hope he had for anyone to help him. He manages to escape but, when he appears before Gingka and his friends, he looks completely battered and passes out immediately after he saw them, as if he's just then finally reached the limit of his energy. He's then captured again and left in a dark room, just being forced to wait for whatever punishment might be coming to him.
The Arrangement, in general. Depending on how compatible you are with it, going through the process can be VERY painful. Even for those that are 100% compatible, the Arrangement brings out, aside from enhanced beyblading skills, intensified negative emotions and, in the cases of Jack and Damian, possible insanity. And let's not even start on what it did to Toby.
The ghastly expression on Julian's face after he crosses the Despair Event Horizon on his battle against Damian.
Continuing on the subject of the dark power, we learn a lot about it in this season when it's discovered that it's infected Tsubasa, bringing out a darkness in his heart that we eventually learn about through flashbacks. Tsubasa's dark side was just completely insane and only wanted to win, no matter what. This lead to the destruction of the entire arena during his and Yu's battle against Damoure and Benkei, as well as knocking out Damoure, Benkei, AND Yu.
Then, later on, we learn the origin of the dark power: It was the dark emotions in the hearts of the people that L-Drago was passed down to through the centuries, including greed, ambitions, anger, and desires of those people. Think about it: a power actually created by the darkness in peoples' hearts...
There's also the nightmare Yu had after the above mentioned battle. A little kid, especially a normally happy one like Yu, dreaming of an entire building going up in flames while he can only stand there and watch. You wouldn't imagine such graphic imagery from the mind of a kid like him.
The entire story of Metal Fury is basically centered around the Apocalypse and, when everything's said and done, the destruction caused during the final battle isn't just magically fixed: it stays around for, presumably, many years after.
And this battle effected the entire world: volcanoes erupted, earthquakes ensued, buildings were destroyed, etc. Also, some people died...this IS a kids' show, right?!
A minor detail in the long run, but a group of tombrobbers who had been tailing Ryuto actually threatened him with knives! In this world where most people use magical spinning tops as a way of settling their disputes, it is at least a bit frightening to see actual deadly weapons being used.