Well, it could still be Thanos. His goal of collecting the Infinity Stones would be a great threat to Superman's world as well. Superman would have to figure out how to stop Thanos from using the stones' power on a galactic scale.
Lex Luthor could also be a main villain in this fanfic. He could team up with Thanos, thinking that he can use Thanos' power to finally defeat Superman. But in reality, he might be used by Thanos.
Metallo could be an interesting villain in this fanfic. His kryptonite - powered body could pose a serious threat to Superman. And he could also target the Furies as they try to help Superman. His mechanical nature and single - minded pursuit of destroying Superman could make for an exciting conflict within the story.
A powerful dark wizard could be the main villain. He could be jealous of the clone's unique powers and want to steal them for himself. He might use dark magic to try and corrupt the clone or simply try to destroy it to prevent it from becoming too powerful.
It could be a new villain that emerges from the power vacuum left by Thanos. Maybe one of his underlings decides to step up and continue his tyrannical ways.
Most likely it would still be Thanos. Since he was the main villain in Infinity War and his actions were the cause of so much destruction, it makes sense that he would continue to be the main adversary in the sequel.
Darkseid would be a great main villain. He's already a powerful and well - known foe in the DC universe. He could be the one who starts collecting the Infinity Stones - like items to gain ultimate power and rule over all universes. His army could also be involved, making it a large - scale war for the Justice League.
Captain America could be the main character. He's always been a leader, and in the aftermath, he could be the one trying to hold the remaining Avengers together. He would be dealing with his own sense of loss and responsibility. He might also be trying to figure out how to prevent future disasters like Infinity War.
Hermione Granger would also be a crucial character. Her intelligence and vast knowledge of magic could be key in understanding the powers of the Infinity Stones and coming up with strategies to deal with them. She could also be the one to communicate with the Avengers if they come to Hogwarts, as she is good at dealing with new and complex situations.
Loki could be a great main villain. He could be secretly fueling the Civil War for his own gain, like trying to take over Asgard while everyone is distracted. He has the cunning and the motivation to do so.
The Kingpin could be a great main villain. He could see the Civil War as an opportunity to expand his criminal empire. He could be secretly funding both sides in a way that makes the conflict worse, all while Spider - Man is trying to figure out his role in the war.
One idea could be Superman teaming up with the Avengers in a way that defies the normal rules of their universes. Maybe he has a unique power that helps them against Thanos, like his super - breath freezing Thanos' army.