It could also be due to external forces. There might be some powerful entities in the fanfiction that don't want Naruto and Rias to be together. They could put so much pressure on Naruto, like threatening the safety of his friends in the Leaf Village, that he has no choice but to leave Rias to protect his people.
One possible reason could be a difference in their goals. Naruto is from the Hidden Leaf Village with a mission to protect it and promote peace there. Rias, on the other hand, has her own responsibilities in the Underworld. Their conflicting duties might lead to Naruto leaving.
Maybe there's a misunderstanding between them. For example, Rias might make a decision that Naruto doesn't agree with regarding how to deal with an enemy. This disagreement could cause Naruto to feel that he can't stay with her any longer and thus leave.
It could also be due to a power struggle. Naruto is extremely powerful and independent. If Rias or other members of the peerage try to control or limit his power in some way, he would not tolerate it. His power is a part of who he is, and he's used to using it freely to protect others. So this could lead to his departure from the peerage.
Maybe it's because of the different power systems. Naruto has chakra and his ninja abilities, and Rias has her devil powers. If in the fanfiction these power systems are not properly integrated or if one overshadows the other in an unappealing way, Naruto could be depicted as hating Rias. Say, if Rias' devil powers are made to seem too overpowering and it goes against Naruto's sense of fairness in combat, it could lead to such a scenario.
In the 'naruto rejects rias fanfiction', Naruto might reject Rias because of their different character traits. Naruto is known for his boisterous, positive, and somewhat naive nature. Rias, as a devil in her own story, has a more complex and often manipulative side. Naruto, with his straightforward ninja values, might not be able to deal with or accept Rias' way of doing things. For example, Naruto believes in hard work and loyalty among his comrades, while Rias' actions might be driven more by power plays and strategic considerations within her devil society, which Naruto could find unappealing.
One reason could be that Naruto might feel he has outgrown Jiraiya's teachings in the fanfiction. He may want to explore his own path independently. Another possibility is that Naruto gets involved in a mission or a situation where he has to part ways with Jiraiya for the greater good. For example, if there is a threat in a far - off land that only Naruto can handle, and Jiraiya has other commitments elsewhere.
One reason could be to seek more power. In some fanfictions, Naruto might feel that the Leaf doesn't offer enough resources or training for him to reach his full potential. So he decides to leave to find a place where he can grow stronger.
One possible reason could be a misunderstanding. Maybe Rias mistakes Naruto for an enemy due to some misinformation. For example, if there's a false rumor that Naruto is planning to attack her group. Another reason might be that Rias is forced to hurt Naruto under some sort of mind control or external pressure. It could also be a situation where Naruto accidentally gets in the way of Rias while she's dealing with a more powerful threat and she has no choice but to harm him in the process.
One reason could be to gain more power. In many fanfictions, Naruto realizes that the threats he faces are far greater than what he can handle with his current skills in Konoha. So, he decides to leave and train in a more secluded and challenging place to enhance his abilities.
Perhaps Naruto has some unresolved issues from his past that he doesn't want to burden his family with. He may think that leaving is the best way to deal with these issues on his own, without putting his family in the middle of his personal turmoil. He might go off on a solo adventure to find himself and come to terms with his inner demons.
One reason could be to seek new challenges. The elemental countries might have become too familiar, and he wants to explore uncharted regions to test his skills further. Another could be to escape from the fame and expectations in the elemental countries. He might feel suffocated by the constant attention and the high standards set for him.
One possible plotline could be that Naruto has his own mission or purpose that is in conflict with Rias's plans or the world she is a part of. So, he decides to leave to pursue his own goals. For example, he might need to go back to the Hidden Leaf to protect it from a new threat that only he can handle. Another could be that Naruto discovers some dark secret about Rias or her group and can't stay with them any longer. He values his own moral code too much to be associated with something he deems wrong.