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.
A third plotline could be about Naruto having to deal with the jealousy and suspicion of others in the ninja world because of his newfound Rinnegan. Some might see it as a threat or a sign that he's becoming too powerful. This would create a lot of political and personal drama for Naruto as he tries to prove that he's still the same person and that he'll use the power for good.
If Naruto got the Rinnegan, he might become more cautious. The power of the Rinnegan is so great that he would realize he needs to be more careful with it. He wouldn't be as brash as before.
A frequent theme is adaptation. When the Rinnegan is introduced into a crossover, characters have to adapt to this new power dynamic. For example, in a Naruto - Harry Potter crossover, the wizarding world has to adapt to the existence of the Rinnegan. Also, redemption can be a theme. A character who has misused the Rinnegan may seek redemption in the crossover story.
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 plot could be that a character from Naruto with the Rinnegan somehow gets transported to the Inuyasha universe. Maybe they team up with Inuyasha and his friends to fight a common enemy. For example, the power of the Rinnegan could be used to counter some of the powerful demons in the Inuyasha world. The character might also introduce new jutsu or abilities to the Inuyasha gang, which could change the way they fight battles.
A main feature is often the overpowered nature of Naruto with the godlike Rinnegan. His abilities are enhanced to a level that allows him to do things like effortlessly defeat powerful opponents. Another feature can be the exploration of new jutsus or techniques that come with this form of the Rinnegan.
One popular 'godlike rinnegan naruto crossover fanfiction' might be 'Naruto: The Rinnegan God'. It combines the powerful concept of the Rinnegan in Naruto's world with a god - like twist. The story often delves into Naruto having enhanced powers due to a special form of the Rinnegan, leading to new and exciting adventures against powerful foes.
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.
There's also 'Naruto and the Rinnegan Legacy'. This fanfic delves deep into the lore of the Rinnegan and how Naruto fits into it. It explores how Naruto uses the powers of the Rinnegan not just for fighting but also for unifying the ninja world. The character development in this fanfic is quite remarkable as Naruto has to adapt to this new power while still staying true to his original self.