Another possible antagonist could be a rogue Uchiha who is jealous that Naruto, an outsider, has gained the Sharingan. This Uchiha might feel that the Sharingan is a sacred power of their clan and should not be in the hands of someone who is not an Uchiha. So, they would try to take it back by any means necessary, even if it means fighting Naruto and his friends.
Danzo could also be a main antagonist. He was always power - hungry and paranoid. Naruto having the Sharingan might make him feel that Naruto is becoming too powerful and unpredictable. So, he could try to eliminate Naruto or control him. Plus, Danzo has a history of using underhanded means to achieve his goals, and Naruto's new power would be a great target for his schemes.
It could be Orochimaru. Since he has always been interested in obtaining powerful abilities, he might see Naruto with the Sharingan as a threat and try to take it for himself.
It could be Orochimaru. He has always been interested in powerful abilities like the Sharingan. In this fanfiction, he might try to steal Naruto's newly acquired Sharingan for his own experiments and to increase his power even more.
Madara Uchiha could be an interesting main antagonist in this crossover. Since he already has strong ties to the Sharingan and was a powerful force in the Naruto series. If he somehow got his hands on the Rinne Sharingan's full power, he would be even more formidable. He could use it to manipulate reality or time, making it extremely difficult for Naruto and his friends to stop him.
It could be a rogue ninja from a forgotten clan who has a vendetta against the Hidden Leaf. This ninja might be seeking to obtain the power of the Mangekyou Sharingan for himself, and sees Naruto as a threat. So, he tries to stop Naruto from fully awakening it and uses all kinds of dark jutsu to attack Naruto and his friends.
Another possibility is that the main antagonist is a group of power - hungry individuals who want to take Naruto's control of the Nine - Tails for themselves. They could be from within Konoha or from other villages. They might try to manipulate Naruto, or if that fails, they'll try to steal the Nine - Tails' power by force. They would likely be very skilled and have some devious plans up their sleeves.
Well, one possibility is that Naruto's new Sharingan power could give him an edge in battles against stronger foes. He might be able to quickly analyze their moves and counter them more effectively.
It could be an evil ninja who also has a powerful form of the Sharingan. He might be jealous of Naruto's new ultimate Sharingan and wants to take it for himself. This antagonist could use his Sharingan powers to create illusions that are so powerful, even Naruto has a hard time breaking free from them.
It could be a rogue ninja who has also obtained a corrupted form of the Rinne Sharingan. This antagonist would use the power for his own gain, causing chaos in the Naruto world. He might be seeking to overthrow all the existing shinobi villages and establish his own rule, using the unique abilities of the Rinne Sharingan like the ability to create powerful illusions that can affect entire villages at once.
In some fanfictions, it could be through a divine intervention by Kami. Maybe Kami sees Naruto's pure heart and his need for more power to protect the village. So, Kami decides to bestow upon Naruto the power of Madara's Sharingan as a way to give him an edge in battles against powerful foes.
A rogue Uchiha who has lost the use of one of his Sharingan eyes due to a failed experiment. He becomes jealous of the protagonist who has one working Sharingan eye and tries to take it for himself. He might use his remaining Sharingan powers in cruel and unexpected ways to try and defeat the protagonist.
It could be Orochimaru. Since he has always been interested in powerful ninja abilities, he might see Sakura with the Sharingan as a new target. He could try to steal the Sharingan from her to add to his own collection of powerful jutsus and abilities.