A time - traveling villain from Chloe's future could come back to Smallville. This villain blames Chloe for something that happened in the future and is determined to stop her from achieving something important in Smallville. This would add an interesting time - travel element to the fanfiction and create a unique antagonist.
An alien entity that has been dormant beneath Smallville for centuries could awaken. This entity could view Chloe and Clark as threats to its plans of taking over the town and the world. It could use its advanced powers to manipulate the townspeople and turn them against Chloe and Clark, making it a formidable foe.
Lex Luthor could be a great antagonist. He's always looking for power and knowledge. If he discovers Naruto's abilities, he might try to use them for his own gain or see Naruto as a threat to his plans in Smallville.
It could be a new villain created specifically for the fanfiction. Maybe someone who has a vendetta against Chloe and targets her because she has the Miraculous.
Another possibility is Clark Kent himself. Their friendship was very strong, and there were always some unspoken feelings between them. A situation where Clark is the father would bring about a lot of emotional turmoil as they both try to figure out how to handle this unexpected development.
I think Rogue would be an interesting main character in a crossover. Her power - absorbing abilities could create some really unique situations, especially when she comes into contact with Clark or other powered individuals in Smallville. On the Smallville side, Lex Luthor could be a main character too. His devious nature and thirst for power could put him at odds with both the X - Men and Clark, making for a complex and engaging story.
If it's a crossover with Alice in Wonderland, the Queen of Hearts could be the main antagonist. The Queen might see Tinkerbell as an intruder and try to behead her. Tinkerbell would have to use her wits and magic to survive in the crazy world ruled by the Queen of Hearts.
One idea could be that Chloe discovers a hidden power in Smallville that is linked to her own family's past. Maybe she stumbles upon an old diary in the Kent barn that reveals secrets about a long - forgotten relative who had a connection to an otherworldly force in Smallville. This could lead to her and Clark teaming up to uncover more about this mystery and protect Smallville from a new threat that is drawn to this newly - discovered power.
A powerful demon from another dimension could be the main antagonist. This demon could be attracted to the power that Sinbad wields in the Magi world and wants to steal it for himself. He could start causing chaos in both the world Sinbad is from and the world he's been transported to in the crossover.
A new character could be introduced as the main antagonist. For example, a being from another dimension who has been observing both Sonic's and Megaman's worlds. This being realizes that by combining the chaos energy from Sonic's world and the advanced robotics technology from Megaman's world, it can create a new, all - powerful empire. So it starts to manipulate events in both worlds to bring about this combination, while Sonic and Megaman have to stop it.
Dr. Eggman and Dr. Wily could team up. Dr. Eggman has his mechanical creations and knowledge of Sonic's world, while Dr. Wily is an expert in creating powerful robots in Mega Man's world. Together, they could be a formidable force against Sonic and Mega Man.
Thanos could be an interesting antagonist in a crossover. Imagine Dr Fate having to use his magic to try and stop Thanos from getting all the Infinity Stones. Thanos' brute force and determination would be a great contrast to Dr Fate's magical finesse.