One possible villain could be Bizarro. Bizarro is always causing chaos and with Superboy and Superman together, it would be an interesting fight. Bizarro's reversed logic and powers would make it a tough battle for them.
In a 'superboy meets superman fanfiction', there could be an epic battle at first as they test each other's powers. Maybe Superboy is initially a bit rebellious and wants to prove himself against Superman. Then they could end up teaming up to fight a common enemy like Lex Luthor or some other powerful villain from the Superman universe.
Some fanfictions explore the idea of a power struggle between them. Even though Superman is more experienced, Superboy might have some unique powers or a different way of thinking. This can lead to some interesting conflicts and how they resolve them, while still maintaining their bond as heroes in the DC universe.
In Young Justice fanfiction, Superman and Superboy often have complex relationships. Superboy might struggle with living in Superman's shadow. He could be constantly trying to prove himself as a worthy hero, not just a clone. For example, in some stories, Superboy takes on dangerous missions alone to show he's as capable as Superman.
They also interact with the rest of the Young Justice team differently. Superman is seen as this big - time hero, while Superboy is more of the up - and - coming, rough - around - the - edges type. In some fanfics, Superboy's relationship with the team helps him grow into his own hero, separate from Superman's influence.
One possible reason could be a misunderstanding. Maybe Superman is under the influence of some mind - controlling villain or a magic spell that makes him see Superboy as a threat when he really isn't. Another reason could be a difference in their ideologies. Superboy might have a more modern or radical approach to saving the world that Superman doesn't agree with, leading to a conflict that gets out of hand.
One interesting story could be about baby Superboy's first attempts at using his powers under Superman's watchful eye. Maybe he accidentally uses his heat vision and sets a small part of the Kent farm on fire, and Superman has to quickly teach him how to control it.
One interesting Superboy x Superman fanfiction could be about Superboy learning valuable lessons from Superman. Maybe it shows Superboy struggling with his powers and Superman guiding him through it. Another could be a story where they team up to face a powerful enemy that neither could defeat alone.
The hurt could also make Superboy more determined to prove himself. He might see this as a sign that he needs to be stronger and more independent from Superman. This could lead to a more competitive relationship where Superboy is constantly trying to outdo Superman, rather than a harmonious mentee - mentor relationship as it was before.
A great plotline could involve Superboy and Superman teaming up against a powerful new villain that neither could defeat alone. They would have to learn to work together and trust each other fully. This would show their different fighting styles and how they complement each other. For example, Superman's experience and calmness in battle could balance out Superboy's more impulsive nature.