Well, a plot could revolve around a Rinnegan - induced time - loop situation. A character, perhaps Sasuke, gets caught in a time - loop where he has to keep reliving a certain period in the Naruto story but with different outcomes each time due to the influence of the Rinnegan. He has to figure out how to break the loop and in the process, discovers new secrets about the Rinnegan and its origin. This could also lead to him changing the fate of some characters who died in the original story.
Well, a cool plot for a Rinnegan Naruto crossover fanfiction could be that there is a rift between the Naruto world and a world where the Rinnegan is more common. Naruto gets pulled into this other world and has to adapt to the different power system there. He meets characters who have mastered the Rinnegan and has to learn from them to find his way back home. Along the way, he discovers a connection between the two worlds that was hidden for centuries.
One idea could be a story where the character with the Rinnegan avatar has to navigate a world where the rules of chakra and bending are combined. For example, they might use the Rinnegan's powers to control different elements in a way similar to how avatars control them in the Avatar world.
One plot idea could be a character with red hair and the Rinnegan being a long - lost descendant of an ancient and powerful clan. They could be on a journey to discover their true heritage and in the process, face off against powerful villains who want to use their unique powers for evil.
One plot idea could be Naruto discovers he has the Rinnegan during a particularly intense battle against a new, powerful enemy. His friends are initially shocked but quickly realize they need to adapt to this new power. Another idea is that the Rinnegan was secretly given to Naruto by an ancient entity as a last - ditch effort to save the ninja world from an impending doom that only Naruto can face with this power.
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 a crossover with the Harry Potter universe. Sasuke with his Rinnegan could be a mysterious new student at Hogwarts. Maybe he's on a mission to find a powerful magical artifact that has a connection to his ninja world. Another plot could involve a crossover with the DC universe. He could team up with Batman, both being brooding and powerful in their own ways. Sasuke's Rinnegan abilities would be a great addition to their crime - fighting efforts.
One idea could be Sasuke traveling to a different dimension where the Rinnegan has different powers and he has to adapt. Maybe he meets an alternate version of himself with a unique Rinnegan ability.
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 a character with the red rinnegan having the power to manipulate time on a small scale. For example, they can rewind a few seconds during a battle to avoid an attack or foresee an enemy's move. Another idea is that the red rinnegan gives the ability to communicate with ancient spirits of the Naruto world, which could lead to uncovering long - lost secrets about the origin of chakra.
One plot idea could be that Naruto and Sasuke discover a new power related to the Rinnegan that can only be accessed when they combine their chakra. Another could be a time - travel plot where they go back in time to prevent the creation of the Rinnegan in the wrong hands. Maybe they have to face an enemy who has a corrupted version of the Rinnegan powers and they must use their own understanding of the power to defeat them.