One of his friends could be the cause, accidentally. Maybe a friend makes a deal with a shady character without realizing the consequences. This deal ends up putting everyone in danger, and Yami gets mad at his friend's naivete and the mess they've created.
In a 'yami gets mad fanfiction', it could be that Yami discovers a betrayal. Suppose he trusted someone deeply in a magical world they inhabit together, and that person has been secretly working against him. This realization makes him extremely mad, and he has to decide how to deal with this traitor while also protecting his friends.
In the fanfiction, Yami could be cursed by an enemy, which makes him sick. His strength starts to fade away. His friends notice the change in him and start to investigate. They discover the curse and search for a way to break it. Along the journey, they meet various characters who either help or hinder them. Yami's condition worsens, but his friends don't give up. Eventually, they find a powerful mage who can break the curse, and Yami is cured, learning valuable lessons about the power of friendship and the importance of being vigilant against enemies.
Physical hurt might come from a powerful magic spell. Let's say an evil sorcerer casts a spell that drains Yami's energy and causes him pain. His struggle to overcome this and regain his strength could be a central part of the fanfiction.
One way to explore this in fanfiction could be through a duel. Maybe his opponent uses a new and powerful card that directly harms Yami. This could lead to his friends, like Yugi, rallying around him to find a way to counter the effect.
Since we don't have much context here, it could be about a variety of things. Maybe Mana has some actions or words that set off Mahad in this fan - made story. It could be set in a magical or fantastical world where their relationship is key. For example, if it's in a world of magic, Mana might use a spell in a way that offends Mahad, or perhaps steal something important from him, leading to Mahad getting mad. The fanfiction could then explore how they deal with this conflict, whether they reconcile or if it leads to further problems in their relationship or the world around them.
He might become withdrawn at first. Since he's used to being in control and having a certain dynamic in their relationship, Bella's anger could shock him into pulling back. He could go off on his own for a while to think about what he did wrong.
It could be Perry the Platypus, in a really unexpected turn. Maybe Perry has to keep some secrets from Phineas for his spy work, and one day those secrets are revealed in a way that makes Phin feel betrayed. This would definitely make him mad.
Maybe Chi - chi is constantly comparing Gohan to Goku in the fanfiction. Gohan has his own identity and abilities, and being compared all the time can be frustrating. He could get mad because he wants to be recognized for who he is, not just as Goku's son. Also, if Chi - chi is interfering too much in his training or friendships, that could also lead to his anger.