Perhaps it's due to a power struggle. Tsunade is the Hokage and Jiraiya has his own independent ways. If Jiraiya does something that Tsunade sees as undermining her authority as Hokage, like going on a dangerous mission without her permission or interfering in village politics in a way she doesn't like, Tsunade could take actions that end up hurting Jiraiya. In fanfiction, the writers often explore such complex power dynamics between characters. Also, it could be a matter of jealousy. If Jiraiya seems to be getting closer to someone else or achieving something that Tsunade secretly desires, it might trigger her to act out against him.
One possible reason could be a misunderstanding. Maybe Tsunade misinterprets Jiraiya's actions or words. For example, if Jiraiya writes something in his book that Tsunade takes the wrong way, she might lash out at him. Another reason could be related to their past. If there are unresolved issues from their earlier days together, like an old argument or a failed mission where they had differences in opinion, it could lead to Tsunade hurting Jiraiya in the fanfiction. It could also be a situation where Tsunade is trying to protect Jiraiya in a strange way. She might think that by pushing him away or causing him physical or emotional pain, she is actually saving him from a greater danger that she foresees.
One possible reason could be a misunderstanding. Maybe Tsunade received some false information about Naruto that made her think he was a threat to the village, so she took actions that ended up hurting him.
It could be due to a misunderstanding. Perhaps there is false information circulating about Naruto that Tsunade believes. Like if someone spreads rumors that Naruto is involved in some dark plot, Tsunade, in her role as Hokage, might take hasty actions against him. Later, when she realizes it's all a lie, she regrets it.
One possible reason could be a misunderstanding. Maybe Naruto overheard some false information about Jiraiya and Tsunade that made him think they had wronged him or someone he cared about. For example, if he heard they were involved in a plot that led to the death of a fellow villager, it could turn his feelings sour.
Perhaps Naruto blames them for some of the hardships he faced. Maybe he thinks that Jiraiya wasn't around enough when he needed a mentor, and Tsunade didn't do enough to support him in certain situations. This could lead to feelings of resentment and hatred in the context of the fanfiction.
One possible plot could be that Tsunade and Jiraiya are deceived by false information about Naruto. Maybe they are made to believe that Naruto has turned to a dark side. For example, an enemy might have created false evidence of Naruto collaborating with a powerful evil force. Tsunade, being the Hokage, and Jiraiya, Naruto's mentor, would then be forced to take actions against Naruto that seem like betrayal from Naruto's perspective.
A possible plot could be that Naruto, under the care of Tsunade and Jiraiya, discovers new aspects of his heritage. Tsunade might know some secrets about the Uzumaki clan that she shares with Naruto. Jiraiya, being his godfather - like figure, helps him explore these new revelations. Meanwhile, the Akatsuki could still be a threat, and Naruto, with his new skills and knowledge, has to fight against them to protect the village and his loved ones.
One possible plot could be that Jiraiya and Tsunade decide to adopt Naruto after seeing his loneliness and potential. They start training him not just in ninja skills but also in life values. Jiraiya might teach him more about the toad sage techniques, while Tsunade could help him with his chakra control and medical ninjutsu knowledge. Naruto would grow up in a more stable family - like environment, which would change his personality a bit, making him more confident and less brash as he has the support and love of two powerful ninjas.
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 possible plot could be that after years of adventures and unspoken feelings, Jiraiya finally decides to settle down. He proposes to Tsunade in a very Jiraiya - style, perhaps writing a novel about their story and presenting it to her. Tsunade, who has always had deep feelings for Jiraiya despite their bickering, accepts. Their married life could be filled with Jiraiya still going on occasional missions while Tsunade manages the village, and they have to navigate the challenges of being in a relationship while having important responsibilities.
In such a fanfiction scenario, it could be due to a misunderstanding. Maybe there was false information spread about Naruto that made Jiraiya and Tsunade believe he had done something unforgivable. For example, an enemy could have framed him for a major crime against the village.