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.
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.
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.
One idea could be a story where a new character is born with the unique combination of Rinnegan, Sharingan and Mokuton abilities. This character could struggle with the power and the attention it brings from different ninja clans. They might be seen as a threat or a savior, depending on who's looking at them.
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.
It changes the story a great deal. First, the Mokuton gives him an edge in combat as he can manipulate plants and wood. This could be used in creative ways like creating huge forests to trap enemies or using wooden constructs for offense. The Rinnegan, on the other hand, is a whole new level of power. He could potentially use it to travel between dimensions, which would open up new plotlines. For example, he could discover new threats or allies in other dimensions. Overall, his character would become more complex as he tries to master these new powers.
You need to have a great plot. It could be about a power struggle. Maybe a new villain emerges who wants to steal all three powers and the protagonist has to stop them. Also, describe the powers vividly. When a character uses Mokuton, explain how the trees grow and what they look like. With the Sharingan, describe the patterns and how it affects the user's vision. And for the Rinnegan, detail the strange abilities it gives. This will make your fanfiction more engaging.
His relationship with Sasuke would likely become more complex. Sasuke might be both jealous and intrigued by Naruto's new powers. Naruto would have to prove that he still values their friendship despite his increased strength. With Sakura, she might see Naruto in a new light, perhaps with a bit more admiration as he now has such rare and powerful abilities.
A possible plot could be that Naruto, with his Rinnegan and Mokuton, is seen as a threat by some of the more traditional ninja clans. They form an alliance against him, but Naruto uses his powers in creative ways to show them that he only wants to use them for good. For example, he uses the Mokuton to create a beautiful forest in the middle of a desolate area, and uses the Rinnegan to heal some of the injured ninjas from the clans that oppose him, winning them over in the end.