It could be that in this fanfiction, Naruto inherits the Rinnegan from a long-lost ancestor, unlocking hidden powers and facing new challenges.
In fanfiction, absolutely. Fanfic writers often like to play with the concepts and powers in the Naruto world. Giving Naruto the true Rinnegan can open up a whole new realm of possibilities for the story. It can change the dynamics of his relationships with other characters, as they might react differently to his newfound power. Also, it can lead to the exploration of different plotlines, such as Naruto having to master the Rinnegan's unique abilities, which could be very different from his already known Sage Mode and Nine - Tails powers.
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.
Some fanfictions suggest that Naruto achieves the Rinnegan as a result of intense training in a new form of chakra control. He might discover a way to tap into a deeper level of his own chakra, which has been dormant all this time. As he delves deeper into this new form of chakra manipulation, his eyes start to change. Over time, with continuous practice and facing numerous challenges that push his limits, his eyes finally transform into the Rinnegan. It could also be that he has a genetic predisposition that was activated by a specific event in the fanfiction, like coming into contact with a particular type of energy or meeting a certain character.
In some fanfictions, Naruto might awaken the Rinnegan through a powerful jutsu overload. For example, if he combines a super - charged Rasengan with some ancient and forbidden chakra - based techniques. This could potentially trigger a genetic or chakra - system shift that results in the awakening of the Rinnegan.
Well, it could be due to a genetic anomaly that was dormant within Naruto all along. Maybe his Uzumaki and Namikaze bloodlines combined in a unique way as he faced extreme challenges in the fanfiction, which then led to the unexpected evolution of the Rinnegan. For example, if he was exposed to a strong and strange form of chakra during a battle with an extremely powerful enemy, this could be the catalyst for such a transformation.
It might be related to a connection with some powerful entity in the Wave arc. For example, if there's a secret shinobi from the past whose power is tied to the Rinnegan and Naruto somehow forms a bond with that power source, it could lead to the awakening. Also, the intense emotions and challenges he faces in the Wave arc might be a catalyst, pushing his chakra to a new level and awakening the Rinnegan.
With the Rinnegan, he could have abilities like the Six Paths techniques. He might be able to use the Preta Path to absorb chakra attacks. And with the Hyoton, he could create ice - based jutsu that are much more powerful than normal ice jutsu, like freezing an entire area instantly.
One possibility could be a time-travel fanfiction where Naruto acquires Mokuton through some ancient technique or encounter in the past.
One implication is that he becomes much more powerful. The Rinnegan gives him access to powerful abilities like the Six Paths techniques, which would change the power dynamics in battles in the fanfiction. He could now face stronger enemies more easily.
It could also be a situation where Naruto's connection to Hagoromo is deepened in the fanfiction. For instance, Naruto might have a vision or a spiritual encounter with Hagoromo. During this encounter, Hagoromo realizes that Naruto is the key to bringing true peace to the ninja world. So, he imparts the power of the Rinnegan to Naruto to help him achieve this grand goal. This would be a more complex and involved process, perhaps involving Naruto learning about Hagoromo's past and his own role in the grand scheme of things.