Sasuke could potentially be an antagonist. With Naruto having the Rinnegan, Sasuke might see him as a threat to his own power and goals. This could lead to a new rivalry between them, different from their previous one.
Madara Uchiha could be resurrected or exist in some form and oppose Naruto. Madara always had grand plans for the ninja world, and Naruto with the Rinnegan could be a major obstacle to his continued schemes. Madara might try to take the Rinnegan from Naruto or find a way to counter its powers.
It could be a rogue ninja from a neighboring village who wants to obtain Naruto's Rinnegan for himself. This ninja has been secretly observing Naruto and sees the potential of the Rinnegan. He then tries to hunt Naruto down during his banishment to take the power.
A new character could be introduced as the main antagonist. This character could be an outcast ninja who has secretly been researching and combining the powers of EMS and Rinnegan. He believes that the ninja world should be ruled by the strongest, and he thinks he is the one. So he starts causing chaos and destruction, and Naruto has to stop him using his own EMS - Rinnegan combination.
It could be Sasuke. I know they are friends in the original, but in this fanfiction, Sasuke might turn against Naruto for some reason. Maybe he becomes jealous of Naruto's newfound power or status.
A new and powerful ninja from a far - off land could be the main antagonist. This ninja has heard of Benihime's power and wants it for himself. He sees Naruto as an easy target at first but soon realizes that Naruto is not going to give up Benihime without a fight. This antagonist could have unique powers that are a challenge for Naruto to overcome while protecting Benihime.
It could be someone who is jealous of Naruto getting the monkey contract. Maybe a rogue ninja who wants the power for himself.
Maybe an old enemy who was thought to be defeated but has somehow returned stronger. Orochimaru could be a possibility. He was always obsessed with power and immortality. If Naruto is revived, Orochimaru might see it as an opportunity to study Naruto's new state of being (since he was revived) and use that knowledge for his own dark purposes.
In some fanfiction concepts, there could be a spiritual or mental connection established between Naruto and Nagato. Since Naruto has this unique ability to understand and connect with people on a deep level. Through this connection, Nagato might pass on the power of the Rinnegan to Naruto. It could be like a transfer of not just the physical power but also the knowledge and understanding that comes with the Rinnegan.
The main antagonist might be an organization that wants to take over the Hidden Leaf Village. They see Naruto as a major obstacle because of his strength and influence among the villagers. So, they devise a plan to make everyone in the village betray Naruto. They use mind - control techniques or spread misinformation on a large scale to achieve their goal. This way, they can weaken the village from within before making their move to take it over.
Sasuke could also be the main character. Given his connection to powerful eyes in the Naruto series, if the Rinnegan was abandoned, Sasuke's role would change significantly. He would have to re - evaluate his own power and place in the ninja world, which could make for a really interesting story with him as the main focus.
It could be an unknown Uchiha who was overlooked in the main story. Maybe they were born with the Rinnegan but due to some political unrest in their village, they were forced to hide their power and were thus neglected. In the fanfiction, they could come out of hiding and shock everyone with their Rinnegan - based abilities.