It could be an old enemy who has resurfaced and found a way to turn Naruto against the Leaf. Maybe Orochimaru, who has always been interested in Naruto's power, manipulates him into attacking the village. Orochimaru could use his knowledge of dark jutsu to influence Naruto's mind.
Perhaps it's a new character introduced in the fanfiction. This character might have a vendetta against the Leaf for some past wrong and sees Naruto as a powerful tool to exact revenge. They could use false information and emotional manipulation to make Naruto believe that the Leaf is his enemy.
The antagonist could also be a group. For instance, a group of rogue ninjas who want to see the downfall of the Leaf. They could kidnap Naruto's loved ones and force him to attack the Leaf under threat. This would create a complex situation where Naruto has to balance protecting his loved ones and not causing harm to the village he once called home.
In this fanfiction, perhaps Naruto could be under some sort of mind control. Maybe an enemy has found a way to manipulate him into attacking the Leaf. It could also be a case where Naruto is misled about the true nature of the Leaf Village, believing it has committed some great wrong that warrants his attack.
It could be Orochimaru. He has always had his eyes on Konoha and might find a way to manipulate Naruto into attacking it. Maybe he uses some new experimental jutsu on Naruto to make him do his bidding.
It could be a rogue ninja from the Hidden Leaf's past who has come back for revenge. Maybe someone who was wronged by the village long ago and has now amassed great power to destroy it. Another possibility is a new enemy from outside the village, like a powerful warlord from a far - off land who wants to conquer the Hidden Leaf for its resources.
It could be a new and powerful trainer who has a vendetta against Ash. This trainer might see Ash as a threat to their own rise to the top in the Pokemon world. They could manipulate Leaf into betraying Ash to further their own goals.
Sasuke could be one to stop Naruto. They have a complex relationship and Sasuke might understand Naruto's motives and be able to talk him down.
A group of rogue ninja who are hunting nekoshou for their special powers could be the main antagonists. They see Naruto's newfound connection with the nekoshou as a threat and try to eliminate him and the nekoshou he is protecting.
It could be a bully in the village. This bully could constantly pick on Naruto because of his status as the Jinchuriki of the Nine - Tails. He might try to steal Naruto's food or prevent him from playing with other kids.
Madara Uchiha could be a great antagonist. His powerful Sharingan abilities and his grand plans for the Naruto world would put him at odds with Supergirl. He might see her as a threat to his control and try to manipulate or defeat her. Another option could be Kaguya Otsutsuki. Her god - like powers and desire to reshape the world would clash with Supergirl's values and her attempts to protect the people of the Naruto universe.
Kabuto could also serve as the main antagonist. He is a sly character. He might enter the race with the intention of gathering data on all the participants, especially Naruto and his friends. He could use his medical ninjutsu to enhance his own racing abilities in unfair ways, like numbing pain to push himself further or using some sort of drug - like jutsu to boost his speed.
A powerful rogue ninja who wants to steal the Nanosuit from Naruto could be the main antagonist. This ninja might have his own reasons, like using the suit to take over the ninja world.