Perhaps the fanfic is exploring an alternate universe concept. In this universe, the relationship between Jiraiya and Naruto has been strained due to different events that didn't occur in the original story. Jiraiya's actions that seem like a betrayal could be a result of different political or personal circumstances in this alternate world. For instance, if there was a power struggle in the Hidden Leaf Village and Jiraiya sided with a different faction for some reason, Naruto would feel betrayed.
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.
Perhaps in this fanfic, Naruto would be more confident earlier in his life. Since Jiraiya is a strong and experienced ninja, his early presence in Naruto's life could provide a sense of security. They might go on missions together earlier, and Naruto could learn about the importance of teamwork and strategy from Jiraiya at a young age. This could potentially change the course of Naruto's development, making him a more well - rounded and powerful ninja much faster.
One possible plot could be that Jiraiya is forced to betray Naruto due to some external threat. Maybe an enemy has captured Jiraiya's loved ones and threatened to kill them if he doesn't turn on Naruto. Jiraiya, in a difficult position, might have to pretend to be against Naruto to protect his loved ones while secretly trying to find a way to free both Naruto and his family from the enemy's clutches.
In such a fanfic, one possible scenario could be that Jiraiya decides to secretly train Naruto during the Chunin Exams. He might teach Naruto some new and powerful jutsu that Naruto then uses to surprise his opponents in the exams. This could lead to Naruto standing out even more and attracting both admiration and envy from other participants.
In such a fanfiction, it could be due to a misunderstanding. Maybe Naruto was forced into a situation where he had to act against the Yugioh world for the sake of his own village. For example, if there was a threat to Konoha that was somehow related to the Yugioh realm and he was given no other choice but to 'betray' them.
Another possibility is a misunderstanding. Maybe some false information is spread about Naruto that makes Tsunade believe he has gone bad. In the world of Naruto, there are often enemies who try to create chaos by sowing seeds of distrust. Tsunade, without fully investigating, could fall for such a trick and seem to betray Naruto.
Naruto would be determined to get to the bottom of it. He would not just accept the betrayal at face value. He would use his skills and the help of his friends to investigate what made Jiraiya turn against him. Naruto's ninja way is about never giving up, and this situation would be no different. He would fight against this betrayal, both physically if Jiraiya became an enemy in combat, and emotionally, trying to understand the reasons behind it all while still holding on to the hope that Jiraiya could be redeemed.
In many fanfics, Anakin's betrayal by the Jedi could be due to a sense of being marginalized. The Jedi Council often treated him with suspicion because of his age and his strong connection to the Force. They didn't fully trust him and this made Anakin feel isolated. For example, they didn't grant him the rank of Master, which he felt he deserved. This sense of being undervalued could be a significant factor leading to his betrayal in fanfics.
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.
Well, one possibility is that Naruto has some kind of premonition in the fanfiction. So he quickly rushes to Jiraiya's location where Pein is attacking. And he uses his shadow clones cleverly, distracting Pein long enough to rescue Jiraiya. He could also have some secret help from a new ally or an unexpected power boost from within himself.