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.
Lex Luthor would be a great choice. He's Superman's long - time nemesis. He could form an alliance with some of Batman's foes like the Joker. Luthor could use his intelligence and resources to create a plan that only Superman and Batman together could stop.
Trigon, Raven's father, could also be the main villain. He might see Superman as a new obstacle in his path to spreading chaos and destruction. His demonic powers would be a huge challenge for both Raven, who has a complex relationship with him, and Superman, who has never faced such a dark and powerful entity from another dimension.
Lex Luthor could be a great antagonist. He could be jealous of their combined power and try to create a device that can split them up or weaken their powers. He might also try to turn the public against them by framing them for crimes they didn't commit.
Lex Luthor would be a great antagonist. He could see Superboy as a threat to his plans in Metropolis and try to find ways to discredit him or even eliminate him. Since Lois is a journalist, she might start to investigate Lex's actions against Superboy, which would put her in danger as well.
Lex Luthor could be a likely main villain. He hates Superman and would see Damian as a tool to use against him. He might manipulate Damian into believing Superman is a threat to Gotham, causing Damian to attack Superman first.
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.
The plot could involve Superboy getting lost in the X - Men's universe. He has to figure out how to get back home while also getting involved in the X - Men's internal conflicts. Maybe there's a power struggle within the X - Men group and Superboy's outsider perspective helps to resolve it. At the same time, he has to deal with the fact that his powers are different from the mutants and some may see him as a threat or an oddity.
The plot could be Superboy discovers Krypto while on a routine patrol. Krypto's super - dog abilities might help Superboy in a fight against a new villain in town.
Lex Luthor would be a great villain. He could be plotting to destroy Superman once and for all while also trying to outsmart Batman. His intelligence and resources make him a formidable foe for both heroes.