Perhaps in the fanfiction, the Sandaime betrays Naruto by revealing his secrets to the wrong people. Like, he tells about Naruto's connection to the Nine - Tails in a way that endangers Naruto. It could be because the Sandaime is trying to protect the village at all costs, even if it means sacrificing Naruto's well - being and trust.
In this fanfiction, the Sandaime might betray Naruto by not fulfilling a promise he made to Naruto's parents. Maybe he was supposed to protect Naruto from all harm and secrecy, but instead, he lets Naruto be exposed to various threats and negative situations in the village, which makes Naruto feel completely betrayed as he thought the Sandaime was someone he could rely on.
One possible plotline could be that Naruto discovers a hidden threat to Sandaime before anyone else. Maybe he stumbles upon a secret enemy's plan while on a mission. He then uses his unique skills, like his shadow clones, to outwit the enemy and save Sandaime at the last moment. For example, he could create a diversion with his clones while he sneaks up on the bad guys and disarms them.
Naruto would probably be extremely hurt. He has always looked up to the Sandaime as a grandfather figure. So, he might initially go into a state of shock and disbelief.
One possible plotline could be that Mei misinterprets Naruto's actions as being a threat to her village. Maybe Naruto's attempts to bring peace and unity among the villages are seen by Mei as him trying to gain too much power. So, she betrays him by spreading false rumors about him, which turns many against Naruto.
In a 'Naruto son of Sandaime' fanfiction, the story could center around the relationship between Naruto and the other clans in the village. As the son of the Sandaime, they might view him differently. Some clans could try to befriend him for political reasons, while others might be jealous or suspicious. Naruto would have to navigate these complex relationships while also dealing with his own growth as a ninja and his desire to be recognized for his own merits, not just because of his father.
One possible plotline could be that Serafall, perhaps influenced by some external force or a misunderstanding, turns on Naruto. Maybe she believes Naruto has some hidden agenda that endangers her or her world. So she starts to undermine Naruto's efforts and even plots against him directly.
In this fanfiction, perhaps Naruto discovers a dark secret about the Wave mission that the higher - ups in Konoha don't want him to know. And when he tries to expose it, they make it look like he's betraying the village to the Wave people, leading to his betrayal.
One plotline could be that Naruto is tricked into believing the Jedi are hiding a great power that could save his world but are being selfish about it. So, he decides to steal it from them, which is seen as a betrayal. Another could be that he falls in love with a character who is an enemy of the Jedi, and for love, he turns against them.
Another plot could involve jealousy. If Sakura becomes jealous of Naruto's growing popularity and power among the villagers, she might betray him. She could spread false rumors about him, which would lead to the villagers turning against Naruto.
One possible scenario is that Naruto would gain a lot more knowledge about the village's history and politics. The Sandaime, being an experienced Hokage, could teach Naruto about the different clans in the village, their relationships, and how to manage them. Naruto might also learn more advanced jutsu more quickly, as the Sandaime could give him personal training. This could make Naruto a much stronger ninja at a younger age and perhaps change the course of some of the earlier story arcs.
In a Naruto fanfiction, Orochimaru could be paired with the Sandaime in a more complex way. Not just as an enemy, but perhaps in a story where the Sandaime tries to redeem Orochimaru. Another character would be Minato. Even though they were from different generations, they both had a connection to Konoha's leadership. You could write about how the Sandaime influenced Minato or vice versa. And Iruka could also be paired with the Sandaime. Iruka is a teacher, and the Sandaime was also very much involved in the education and growth of the shinobi in Konoha. So, a story about how the Sandaime and Iruka work together to improve the academy or deal with problem students could be really interesting.