A possible fanfiction could involve a new villain who is after both the power of the Sharingan in the Naruto world and the firebending abilities of Azula in the Avatar world. Naruto and Azula are forced to work together. Naruto uses his Sharingan - like perception skills (if he somehow acquires a form of it) to anticipate the villain's moves, while Azula uses her firebending skills. Along the way, they teach each other about their respective worlds and powers.
In a fanfiction, Azula could be transported to the Naruto world. The Sharingan users would be very interested in her abilities as she is a powerful firebender. Naruto, being the main character, could try to befriend her. He might see her as a lost soul like some of his other friends in the past. The Sharingan could be used to analyze her fighting style and Naruto could learn from it to develop new jutsu. They could team up against common enemies in the Naruto world.
Another fanfiction could involve a situation where Azula is transported to the Naruto universe. She might mistake the lava - based attacks in the Naruto world as some advanced form of firebending. Naruto and his friends would be both curious and cautious about this powerful newcomer with her unique abilities related to fire and Naruto's lava - like jutsu could play a role in their interactions.
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 crossover where Naruto, with his Mokuton abilities, somehow ends up in the Avatar universe and meets Azula. Maybe he tries to use his Mokuton to counter her firebending in a big battle. Another could be a story where Azula discovers a way to use Mokuton-like powers through some dark magic and Naruto has to stop her from misusing it.
A fanfiction could revolve around a young ninja who is born with both the Sharingan and the Rinnegan. He has to hide his powers from the world as he is hunted by those who want to use his powers for evil. As he grows, he meets Naruto and they form an unlikely alliance. Together, they train to master his unique abilities and fight against the forces that seek to destroy them.
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 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.
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 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.