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 rogue ninja who has mastered some dark and forbidden jutsu. He wants to use the clone's power to open a portal to a dimension of chaos. He believes that by controlling the clone, he can gain access to unlimited power and reshape the world according to his own twisted vision.
It could be Orochimaru. He's always been interested in power and new forms of jutsu. Seeing Naruto with Superman - like powers would make him want to either steal those powers for himself or find a way to use Naruto as a tool in his experiments.
A possible main antagonist could be a powerful alien who sees Naruto as an abomination. This alien might come from Krypton and believe that Naruto, as a clone of Superman, is a perversion of their species' power. The alien would have all the typical Kryptonian powers but with a more malevolent intent. He would try to destroy Naruto and the Hidden Leaf Village, thinking that he is doing a service to the universe by eliminating this 'false' Superman.
Well, perhaps it could be about Naruto getting Superman - like powers. Maybe he could fly around Konoha like Superman soars over Metropolis. He might use his super strength to protect the village from threats that are too powerful for normal ninja skills.
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.
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.
One idea could be that the clone has the powers of both Naruto and Superman. For example, it can use Naruto's shadow clone jutsu while also having Superman's super strength and flight. It could be a hero in a world where both Naruto - style ninjas and super - powered beings exist, fighting against a common enemy that threatens both worlds.
One possibility could be that Naruto somehow gains Superman - like powers. Maybe through some strange scientific experiment or a magical encounter. He could then use his newfound abilities, like super strength and flight, in combination with his ninja skills. For example, he might use super speed to perform his shadow clone jutsu even faster, overwhelming his enemies in a way that was not possible before.
Maybe an ancient evil spirit that has been awakened due to some mistake. It targets Ageha because she has a pure and powerful chakra. Naruto, being the hero he is, tries to fight the spirit, but he quickly realizes that he needs Ageha's help as well as the help of all his friends to defeat this powerful foe.
The main villain could be Darkseid. Imagine if he somehow finds a way to enter the Naruto universe. He would be a formidable foe for both Naruto and Supergirl. His omega beams and immense strength would be a huge challenge for them to overcome.
It could be a rogue ninja from the village with the Tenshikage. Maybe he's jealous of the Tenshikage's power and wants to take it for himself. He could be causing chaos in the village, stealing important ninja scrolls and attacking innocent villagers.