Perhaps a plot where Naruto's Rinnegan is a result of a curse placed on him by an ancient evil. As Hokage, he has to not only fight against external threats but also the inner struggle of controlling the power of the Rinnegan without succumbing to the curse. He could learn about the origin of the Rinnegan from old scrolls and seek the help of sage-like characters to overcome the curse.
One idea could be a story where Naruto has to face a new, powerful and mysterious enemy that has the ability to manipulate time. This would put his skills as a Hokage to the ultimate test.
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 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.
One idea could be exploring the Shodai Hokage's early days as a ninja, before the founding of the village. Maybe show his training and how he developed his unique skills.
One idea could be Naruto having to deal with a new and powerful enemy while still adjusting to his role as the 5th Hokage. Maybe this enemy has a unique jutsu that can disrupt the village's chakra network. Another idea is Naruto using his new position to reform the shinobi education system in the village. He could introduce new training methods that focus on teamwork and moral values as well as combat skills.
One idea could be Naruto as Hokage facing a new threat that only Hinata's unique skills can help with. For example, a mysterious enemy that can nullify normal ninjutsu, but Hinata's Byakugan - based techniques are effective. Another plot could be a time - travel fanfic where Naruto and Hinata go back in time and have to prevent a disaster that would change the future of the Hidden Leaf Village. They could also explore their relationship in a different era.
One idea could be that Sakura becomes Hokage first. Naruto goes on a long-term mission and during his absence, Sakura steps up and proves herself as a great leader. She implements new medical ninja programs in the village. When Naruto returns, he is proud of her and they work together to make the village even better.
One idea could be Naruto and Sasuke teaming up to face a new, powerful and ancient threat that even the combined might of the Hidden Villages can't handle easily. They have to use their unique skills and the bond they've reforged as Hokage and his equal.