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Tearjerker: Metal Fight Beyblade
Metal Fusion/Metal Fight
Kyoya's defeat at the hands of Ryuga qualifies both as this and as Nightmare Fuel.
Tsubasa and Yu in the hospital after they were attacked by Damian.
The whole story between Team Dungeon, from Toby having a dangerous illness to Zeo feeling abandoned by Masamune, to them fighting as enemies in the tournament, to them all getting back together. The last part also doubles as a Crowning Moment of Heartwarming.
Yu having to witness Tsubasa's gradual change due to the dark power. Especially when you consider that he's already seen the dark power change one person he had considered a best friend who had ended up betraying him and was now seeing that he might lose another person he'd become a good friend with to the dark power.