In a fanfiction plot, Naruto having the Rinnegan and Sharingan could lead to a situation where he is hunted by other ninja villages who fear his power. He then has to use his new abilities to protect himself and his village. He could use the Sharingan to anticipate their attacks and the Rinnegan to counter them with powerful defenses. Another idea is that he uses the two eye powers to create a new form of chakra that can heal the land damaged by previous battles. This new form of chakra could also be used to strengthen the bonds between ninja from different villages, leading to a new era of peace in the ninja 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.
Another plot could involve a forbidden jutsu that combines the powers of these three ocular abilities. Maybe a hidden scroll is discovered that details how to perform this jutsu, but it comes with a great cost. The main character has to decide whether to pursue this power despite the risks, which could lead to internal conflict as well as conflict with other characters who oppose this dangerous path.
One interesting plot idea could be a story where a character with both Sharingan and Rinnegan has to face an ancient evil that threatens the entire ninja world. This character could struggle with the power and the different abilities of both eyes as they try to master them in order to defeat the enemy.
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.
Imagine a plot twist where the Sharingan and Rinnegan are not unique to the ninja world. In a fanfiction, it could be revealed that an alien race has similar powers. A character from Naruto's world travels to this alien planet and discovers that their understanding of these powers is completely different. They must then adapt to this new knowledge and use it to save both worlds from a common enemy that is drawn to the power of the Sharingan and Rinnegan.
A plot development might involve Naruto struggling to control the Rinnegan at first. Sasuke, noticing this, believes he can defeat Naruto easily with his Sharingan. But as Naruto starts to master the Rinnegan, he shows new abilities that shock Sasuke. This could lead to a situation where they have to team up against a common enemy who is after the power of both the Rinnegan and the Sharingan. Or perhaps a prophecy is revealed that states only one of them can keep their dojutsu power and they must fight to decide who keeps it, leading to a moral and power - based struggle.
One potential plotline could be Naruto using his new powers to finally bring true peace to the ninja world. He could use the Sharingan to understand the root causes of conflicts by seeing through people's true intentions and the Rinnegan to reshape the world in a more harmonious way.
A cool plot could be that a new villain emerges who has the ability to nullify the powers of the Sharingan and Rinnegan. Naruto and Sasuke have to find a way to overcome this without relying solely on their eye powers. They might discover ancient techniques that their predecessors used before the existence of these eye powers.
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.