One likely antagonist could be Chazz Princeton. He's often shown as a bit of a bully in the Yugioh series, and he might target Syrus out of jealousy or just to assert his dominance. Another could be an original character created by the fanfiction writer, perhaps a new student at Duel Academy who has a vendetta against Syrus for some reason. The Society of Light could also be antagonists in a sense, as they might try to manipulate Syrus or use him in their schemes, which could lead to him getting hurt.
One common plotline could be Syrus facing bullying at Duel Academy which causes him emotional hurt. Maybe some upperclassmen pick on him for his dueling skills or his timid nature. Another could be Syrus getting hurt in a dangerous duel, like against a powerful opponent who uses underhanded tactics. Also, he might get his heart broken in a romantic sub - plot within the Yugioh world, perhaps by someone he has a crush on who doesn't return his feelings.
A plot could involve Hell Kaiser being sent to evaluate Syrus for some special training program. As he watches Syrus, he discovers that Syrus has some unique qualities that could be both an advantage and a disadvantage. There could be a conflict where Hell Kaiser has to decide whether to report accurately or help Syrus overcome his weaknesses first. The story could also include duels where Syrus shows his growth under Hell Kaiser's watchful eye.
One possible plot could be that Syrus, while exploring an ancient library in the Duel Academy, stumbles upon a hidden spellbook that has a connection to the Dark Magician Girl. He accidentally summons her in a weakened state. Then, they have to work together to regain her full power while facing various challenges from other duelists who want to capture the Dark Magician Girl for their own purposes.
Yes, there are likely some out there. You can start by checking fanfiction websites like FanFiction.net or Archive of Our Own. Just search for 'hell kaiser watches syrus' in the Yugioh section and you might find some interesting stories.
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.
Their interaction could start with Syrus having a strange dream about the Dark Magician Girl. When he wakes up, he starts noticing little signs around the Duel Academy that seem to be related to her. One day, while dueling, he makes a move that somehow creates a small rift in the magic world, and the Dark Magician Girl steps through it for a brief moment. That moment of eye contact is the start of their interaction.
In a Yugioh GX fanfiction where Aster gets hurt, it could be during a duel. Maybe his opponent uses a powerful card that backfires on Aster, causing him physical or mental harm. For example, a card that creates an illusion of his worst fears, making him stumble and get injured as he tries to escape the illusion.
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.
It's quite normal. In a fandom, people are interested in different aspects of the characters. Zane might be curious about Syrus's backstory, relationships, or potential storylines that fanfiction writers have created. It's just another way of engaging with the fictional world they are part of.