Another possibility is that it's a result of some strange chakra experiment gone wrong (or right). Scientists in the Naruto universe are always dabbling in chakra research. Maybe an experiment meant to enhance her natural abilities instead gives her the Rinnegan, and she then has to learn to control it quickly to avoid being consumed by its power.
One possible antagonist could be a rogue ninja who also wants the power of the Rinnegan. He might see Naruto as a target to either steal the power from or eliminate so that he can be the most powerful in the ninja world. This character could be a new creation or an existing villain with a new motivation.
Definitely. In some fanfics, Naruto uses the Rinnegan to rewrite the rules of ninjutsu. He could develop new techniques that are based on the Rinnegan's abilities, such as the ability to revive the dead in a different way than the traditional Edo Tensei. This makes him a target for those who oppose such a radical change in the ninja world.
The Sage of Six Paths himself could be the key character. Since the Rinnegan was originally his power, he could appear in the fanfic in some form, like a spirit or a time - traveling version of himself. He could then directly bestow the Rinnegan upon Naruto, seeing Naruto's potential and the need for such power to maintain the balance in the ninja world.
Sasuke might be the first to discover it. Since they are rivals and friends, he would be very attuned to Naruto's changes. Sasuke has his Sharingan which can detect power differences, so he could sense the new power of the Rinnegan within Naruto.
In fanfiction, the idea of Naruto having the Sharingan and Rinnegan is often a creative and out - of - the - box concept. It could be due to some kind of powerful jutsu or a unique plot device. Maybe a powerful enemy uses a forbidden jutsu that somehow transfers the powers to Naruto. Another possibility is that in an alternate universe created by the fanfic writer, the rules of chakra and kekkei genkai are different, allowing Naruto to possess these powers.
Yes, there are. You can find them on various fanfiction websites like FanFiction.net or Archive of Our Own. Some of these fanfictions explore unique storylines where Naruto gains the Eternal Rinnegan and how it changes his abilities and the Naruto universe as a whole.
I think Kakashi could also be an ally. Kakashi has a wealth of knowledge and experience, and he would be able to offer strategic advice to Naruto. Also, given his own Sharingan experiences, he might be able to help Naruto better understand and control the Rinnegan. Shikamaru is another possible ally. His intelligence and strategic thinking would be invaluable in helping Naruto make the best use of his Rinnegan powers in various situations, like in battles or in diplomatic negotiations within the ninja world.
It could be Sasuke. If he were to turn to the dark side in the fanfiction, his Rinnegan powers could be used to destroy Konoha. He has the potential to be extremely powerful and if he has some sort of vendetta or is influenced by some dark force, he might take his anger out on the village.
Naruto would probably win. He has an indomitable will and has always found ways to overcome powerful foes. His experience and the unique powers he might gain with the Rinnegan could give him an edge over Madara.