Another storyline could be that Athena accidentally causes harm to one of Naruto's friends. Naruto, being extremely loyal to his friends, immediately blames Athena and his hatred for her starts from there. Even if it was an accident, Naruto's hot - headed nature in some aspects might make him hold a grudge. And as the story progresses, this hatred could grow deeper as Athena tries to make amends but fails to do so in a way that Naruto can accept.
Maybe in the fanfiction, Athena and Naruto are pitted against each other in a battle for control over a powerful artifact. Naruto believes Athena wants to use the artifact for her own gain, which is against what Naruto stands for. This misunderstanding causes him to hate her. The artifact could be something that has the potential to change both their worlds, and Naruto is determined to keep it out of Athena's hands.
One possible storyline could be that Athena appears in the Naruto world and starts interfering with the ninja villages. She might try to impose her own set of laws based on Greek mythology, which Naruto sees as a threat to his people and their way of life, thus leading to his hatred. For instance, she could demand that the villages stop using chakra in a way she deems inappropriate according to her values.
One possible storyline could be that the Si OC is a shinobi from a village that has been wronged by Konoha in the past. They see Naruto as a symbol of Konoha's power and thus direct their hatred towards him. For example, if their village was raided by Konoha in the past for some reason, they hold a grudge against all things Konoha, including Naruto.
There could also be political reasons. Some factions within Konoha might have seen Naruto as a tool or a threat to their own political power. His influence and popularity could have disrupted the existing power balance, leading to animosity from those who wanted to maintain the status quo.
One possible storyline could be how the Hidden Leaf Village copes with his death. Maybe there are power struggles as different clans vie for leadership in the absence of Naruto's unifying presence.
One possible storyline could be that Kalawarner somehow ends up in the Naruto universe. She might be confused at first but then use her own skills to help Naruto and his friends in a battle. Maybe she has some unique powers that are useful against a new enemy.
One possible reason could be jealousy. Maybe in the fanfiction, Naruto feels overshadowed by Sasuke in Sakura's eyes, which leads to his hatred. Another reason might be that he perceives their relationship as a threat to his own bonds with them. For example, he could think that Sasuke and Sakura's closeness excludes him in some way.
In a Naruto fanfiction, Jaune Arc could start his own ninja clan. He could use his knowledge from RWBY to create a new style of combat that combines aura and chakra. Maybe he falls in love with a kunoichi and has to deal with the cultural differences between his world and the Naruto world while also facing off against powerful villains who want to steal his new - found ninja techniques.
One possible storyline could be Naruto struggling to balance his ninja duties with raising his child alone. Maybe he has to take the kid on missions sometimes, teaching the little one about the ninja world along the way. Another could be Naruto dealing with the judgment of the village as a single father, showing how he overcomes that and still raises a strong and kind - hearted child.
Well, in Naruto fanfiction, if there's a neglected baby, it might be that the baby is the offspring of a missing - nin. The village, fearing the baby could grow up to be like its parent, neglects it. Maybe the baby has a chakra nature that is considered 'cursed' in the Naruto world, like some form of dark chakra. As a result, the people around avoid the baby, leaving it to fend for itself in a cruel environment.
Perhaps in a fanfiction, Naruto discovers some dark secrets about his parents that shatter his world view and send him into a depressive state. Temari, being a friend, comes to Konoha on a diplomatic mission and finds Naruto in this state. She tries to help him by sharing her own experiences of dealing with difficult family situations. However, the more she tries, the more she realizes how deep Naruto's pain is and she herself starts to feel a bit depressed due to her inability to fully help him.
Well, in some fanfictions, Itachi might seem to be cheating on Naruto in the sense that he's forming closer alliances with other characters for strategic purposes. For example, he could be getting involved with another ninja clan to gain information or resources for the greater good, but Naruto misinterprets his actions as being unfaithful in their friendship.