Well, it might be the result of a powerful curse or a blessing from a god - like being. In the Naruto universe, there are many powerful entities. If one of them decided to bestow this unique power on Naruto, it could lead to the development of the red Rinnegan. Another idea is that it could be a side - effect of a new jutsu he tries to master. Some jutsus have unforeseen consequences, and this could be one of them.
One possible plot could be that Naruto discovers a hidden power within himself that unlocks the Rinnegan. This new power could make him face new and even more powerful enemies. He might have to learn to control the Rinnegan's abilities, which are different from his normal chakra powers. For example, the Rinnegan can allow for space - time manipulation. Naruto would struggle at first, but with the help of his friends, he would gradually master it and use it to protect the Hidden Leaf Village from a new threat that only the Rinnegan - powered Naruto can defeat.
The plot could start with Naruto suddenly awakening both the Mokuton and Rinnegan. He is confused at first but quickly realizes the potential. He could use the Mokuton to terraform the land, creating fertile areas for farming in war - torn regions. With the Rinnegan, he might be able to communicate with the spirits of past Hokages in a new way. This leads to him uncovering secrets about the ninja world that were long forgotten. He then uses this knowledge and his powers to bring about a new era of peace, where the different ninja clans work together more harmoniously.
The fanfiction could involve Naruto's Golden Rinnegan being the key to a long - lost prophecy. He might find out that his new - found power is the only thing that can stop an ancient evil from awakening. Along the way, he would have to learn how to use the different abilities of the Golden Rinnegan, like being able to see the true intentions of people just by looking at them, which would help him in making allies and avoiding traitors.
The plot could involve Naruto being sent to an alternate dimension where the blue Rinnegan is a common power among a group of powerful beings. There, he has to learn to use his blue Rinnegan to survive and also to find a way back home. Along the way, he meets different characters who teach him unique ways to harness the power of the blue Rinnegan, and he returns to his world with new skills and knowledge.
It could be a result of a magical experiment gone wrong. Some rogue ninja or a mad scientist - type character in the Naruto universe might have been trying to create a super - being and accidentally gave Naruto red angel wings.
One possible plot could be that Naruto is born with red hair due to some strange genetic mutation in the Uzumaki clan. He then somehow gains the Rinnegan, perhaps through a powerful encounter or a hidden inheritance. With these new features, he might face challenges from both within the village who are suspicious of his new powers, and from outside threats who see him as a greater threat or a valuable asset. He could embark on a journey to master these powers and prove himself a worthy protector of the village, all while facing off against new and old enemies.
One origin could be a genetic mutation within the Uzumaki clan that has been dormant for generations. Naruto, being an Uzumaki, could be the first in a long time to have this mutation manifest as claws. Or it could be due to a curse placed on him by an enemy. However, instead of weakening him, the curse gives him the claws which he then learns to use to his advantage. It could also be a gift from a powerful sage or spirit that he encounters during one of his adventures, seeing the potential in Naruto and bestowing him with the ability to have claws for a specific purpose like protecting the village or fighting a greater evil.
Perhaps it was a gift or a curse from some powerful being. For example, a god or a demon could have bestowed this third eye upon Naruto for some purpose, either to help him in his journey or to make his life more difficult with new powers that come with their own challenges.
A new character could be a great protagonist. Maybe an orphan who discovers they have the red rinnegan after a near - death experience. This character would be starting from scratch, with no knowledge of their power, and have to learn and grow while facing the challenges and prejudices of the ninja world.
One implication is enhanced combat abilities. The Rinnegan has various powerful techniques, so Naruto would become an even more formidable fighter. For instance, he could use the Six Paths techniques more effectively.