One idea could be that Naruto discovers he has these powers due to some ancient curse or blessing. He then has to hide it from his friends at first because he doesn't understand it. As he starts to master it, he uses it to protect the village in unexpected ways, like using Mokuton to quickly rebuild damaged areas after an attack while using Sharingan to detect any remaining threats.
Perhaps Naruto is sent to a parallel dimension where all ninjas have unique combinations of powers, and there he discovers his Sharingan and Mokuton abilities. He has to learn to use them quickly to survive in this new world. He befriends some of the local ninjas and together they face a great evil. Naruto uses his Mokuton to create natural defenses for their base and his Sharingan to analyze the enemy's weak points, ultimately saving the parallel dimension and bringing back some new techniques and ideas to his own world.
An interesting plot could be that Naruto, with his new eyes, discovers a hidden conspiracy in the ninja world that was related to the origin of the Rinnegan and Sharingan. He has to use both his powers to uncover the truth and stop those behind it. For example, he might find out that there is a group that wants to control all the powerful ocular jutsu in the world. With the Sharingan, he can detect their lies and with the Rinnegan, he can take on their powerful minions. Also, he could use the powers to communicate with ancient ninja spirits and gain their wisdom to solve current problems.
In a fanfiction, what if a Sharingan user discovers a way to transplant Mokuton cells into their body to gain the ability? However, they soon realize that the combination is not as easy to control as they thought. The Mokuton starts to take over their body, and they have to find a way to either master it or reverse the process. They might seek help from old allies of Naruto or explore ancient ninja scrolls for a solution.
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.
One interesting plot could be the main character exploring the unique abilities of Mokuton Sage Mode in new and unexpected ways. For example, they might discover how to combine it with other ninja techniques to create powerful new jutsus.
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.
Well, in the vast world of Naruto fanfiction, it's possible. Some fans like to combine different elements in unique ways for their stories. But finding ones specifically with Naruto having Mokuton and Sharingan in a yaoi setting can be a bit tricky. You might have to search through different fanfiction websites and dig deep into the Naruto fanfiction section, filtering for the yaoi genre and the specific abilities. Also, keep in mind that the quality of such fanfictions can vary greatly.
Maybe the Mokuton Prodigy is tasked with restoring a forest that has been destroyed by dark magic. Along the way, they face various challenges and make new allies. This could involve battles with creatures corrupted by the dark magic and learning new Mokuton techniques to revive the forest.
One idea could be that Naruto discovers his mokuton abilities can create a special forest that only Hinata can enter. In this forest, they train together and their bond deepens as Naruto shows Hinata the unique powers of the mokuton. Another could be that an enemy attacks the village and Naruto uses his mokuton to protect Hinata, and this event makes them realize their true feelings for each other.
One idea could be that Naruto, with his Mokuton abilities, gets transported to the DC universe. He might team up with Green Arrow in Star City. Since Naruto can create and control plants, he could help Green Arrow by using the Mokuton to create natural barriers during battles or to track enemies by sensing their movements through the plants. Another plot could involve Naruto meeting Poison Ivy. They could have an interesting dynamic as both have a connection to plants. Naruto might try to convince her to use her powers for good instead of causing chaos.
One idea could be that the character with the Sharingan is banished due to false accusations of using its power for evil. He then has to journey alone, facing challenges and learning to control his power in new ways. Maybe he meets a group of outcasts who he befriends and together they fight against the unjust system that banished him.