One idea could be a story where a character discovers a way to combine the powers of the Rinnegan and Sharingan. For example, they might be able to use the Sharingan's precognitive abilities to enhance the Rinnegan's control over the six paths. This could lead to new and unique jutsu that no one has ever seen before.
A fanfiction could focus on a young ninja who inherits both the Rinnegan and Sharingan through some unforeseen genetic quirk. He then has to struggle with mastering these powerful eyes, as they attract the attention of both friends and foes. He might face challenges like being ostracized by his village because they fear his power, but also having to fight off those who want to steal his eyes.
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 idea could be a story where Naruto somehow acquires the Mangekyou Sharingan and Rinnegan. He then has to learn to control these new powers while facing an ancient evil that only he can defeat with the combined might of these dojutsu. Maybe he teams up with Sasuke, who also has his own power upgrades, and they have to figure out how to merge their abilities to save the ninja world.
One idea could be a story where Sasuke, with his Sharingan, discovers a new power related to the Rinnegan that was hidden within Naruto all along. Maybe Naruto has some dormant Sage of Six Paths energy that when combined with Sasuke's powers, they can unlock a new level of strength to fight a powerful, unknown enemy.
One idea could be a story where Naruto somehow acquires the Rinnegan and combines its powers with the Susanoo. Maybe he has to face an extremely powerful enemy that can only be defeated by this new, super - powered combination. He could start by accidentally awakening the Rinnegan during a battle and then discovers that he can merge it with his Susanoo - like form.
One idea could be that Fuu discovers a hidden power within Naruto's Rinnegan that can open a portal to a different dimension filled with ancient ninja secrets. She then teams up with Naruto to explore this new world and face the challenges within.
One idea could be a story where Naruto discovers a hidden power within his Rinnegan that allows him to communicate with the Shinigami. Maybe he needs to make a deal with the Shinigami to save his friends from a powerful enemy. The Shinigami could offer Naruto a special jutsu in exchange for something precious to him.
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.
A great fanfiction concept might be that Naruto somehow gains the Sharingan and Susanoo abilities. Maybe through some sort of experimental jutsu gone wrong (but in a good way). He then has to learn to control these new powers while still maintaining his own Sage Mode and Nine - Tails chakra. It would be interesting to see how he combines these different power sources to fight against new and old enemies.
A fanfiction could be set in an alternate universe where the Sharingan and Byakugan have different powers than in the original Naruto series. For example, the Sharingan could be used to directly communicate with the spirits of the dead, and the Byakugan could see into different dimensions. A young ninja discovers these new abilities and has to use them to save his village from a mysterious threat.
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.