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.
Well, it could be a former ally of Naruto who becomes jealous of his new powers. This person, let's say Sasuke for example, could be corrupted by the idea that Naruto now has powers that are far greater than his. So he turns against Naruto and tries to take his Mokuton and Rinnegan powers for himself. Another antagonist could be a mysterious figure from Naruto's past that has a vendetta against his family and now that Naruto has these powerful abilities, they see it as the perfect time to exact revenge.
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.
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.
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.
The plot could start with Naruto suddenly awakening both the Mokuton and Rinnegan. He is confused at first but quickly realizes the potential. He could use the Mokuton to terraform the land, creating fertile areas for farming in war - torn regions. With the Rinnegan, he might be able to communicate with the spirits of past Hokages in a new way. This leads to him uncovering secrets about the ninja world that were long forgotten. He then uses this knowledge and his powers to bring about a new era of peace, where the different ninja clans work together more harmoniously.
With Mokuton, Naruto could grow trees instantly for various purposes like creating shelters or using them as weapons. And with Rinnegan, he might be able to use the Deva Path to control gravity, push or pull enemies. He could also use the Asura Path to create mechanical arms or other body parts for enhanced combat.
A fanfiction could center around a battle between two powerful ninjas, one who has mastered the Mokuton and Sharingan, and the other who has the Rinnegan. The fight could be not just about physical combat but also about the clash of different ideologies related to these powers. The one with the Mokuton and Sharingan might believe in a more traditional view of power, while the Rinnegan user could have a more radical view.
One plot idea could be a story where Naruto discovers he has the Mokuton and Rinnegan abilities due to some ancient curse or prophecy. He then has to learn to control these new powers while facing off against a new, powerful enemy that is immune to normal jutsu. Another idea is a fanfic where Naruto uses his Mokuton and Rinnegan to travel to different dimensions to find a way to save the Hidden Leaf from a looming disaster. Or perhaps a story where he has to team up with old enemies who are also intrigued by his new powers and together they form an uneasy alliance to fight a greater evil.
It could be a new character created specifically for the fanfiction. A young ninja from a small, unknown village who has the rare Mokuton ability and decides to enter the Chunin Exams to prove himself.