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.
One idea could be that Naruto somehow gains the EMS (Eternal Mangekyou Sharingan) and Rinnegan powers simultaneously. Maybe through some ancient jutsu experiment gone wrong/right. He then has to learn to control these new powers while facing an old enemy who has also gained a new and dangerous power. This would lead to epic battles and Naruto exploring new ways to use these combined powers, like using EMS - enhanced speed with Rinnegan - based space - time ninjutsu.
One possible main antagonist could be a rogue ninja who also has a connection to the Mokuton or Rinnegan powers. Maybe he was once part of a secret experiment that went wrong and now he wants to take Naruto's powers for himself. Another option could be an ancient being that was sealed away long ago and is now awakened by Naruto's new powers. This being could see Naruto as a threat to its plans of world domination.
It could be a new character who is jealous of Naruto's newfound power of the Rinnegan. Maybe someone who has been in the shadows all along and now sees Naruto as a threat to their plans for world domination.
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.
In fanfiction, one way to combine EMS (Eternal Mangekyou Sharingan) and Rinnegan powers could be through a powerful jutsu. For example, a character might create a new form of ninjutsu that draws on the unique abilities of both. The EMS could provide enhanced visual perception and the ability to cast powerful genjutsu, while the Rinnegan could offer control over different elements and the six paths techniques. They could be combined in a way that allows for teleportation between different dimensions, using the space - time manipulation aspects of both powers.
Danzo could be a great antagonist. If Naruto travels back in time, Danzo's schemes and thirst for power would still be there. He might see Naruto as a threat to his plans of controlling Konoha and try to eliminate him. His underhanded methods and shadowy operations would make him a formidable foe for Naruto, especially when Naruto is trying to change the past for the better.
It could be interesting to see Naruto with both EMS and Rinnegan in fanfiction. Naruto is known for his Uzumaki vitality and his ability to master new powers quickly. Having EMS and Rinnegan would give him an entirely different set of skills. He could combine the Rasengan with Rinnegan - based techniques and use the EMS - enhanced perception to dodge attacks even better. His positive attitude and never - give - up spirit would make for an exciting exploration of these powers.
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.
It could be a new character, a rogue ninja from a long - lost clan. This antagonist might have a vendetta against Naruto because they see his potential to awaken the Rinnegan as a threat to their own plans for power. They could be trying to stop Naruto from achieving this new level of power so that they can carry out their evil deeds unopposed.
One possible antagonist could be a rogue ninja who also wants the power of the Rinnegan. He might see Naruto as a target to either steal the power from or eliminate so that he can be the most powerful in the ninja world. This character could be a new creation or an existing villain with a new motivation.