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.
Perhaps Naruto discovers a dark secret about the Jedi that makes him lose faith in them. This could be something like the Jedi using unethical means to maintain their power. He then decides to expose them, but the Jedi see this as a betrayal. In the process, he might team up with some of the Jedi's adversaries who seem to share his new - found views. This could lead to a full - blown conflict between Naruto and the Jedi.
Well, in this fanfiction scenario, the Jedi Council could betray Naruto because they misunderstand his ninja way. The Jedi are all about peace through control and discipline, while Naruto is more about passion and believing in others no matter what. This clash of ideologies could lead the Council to think Naruto is a danger, so they betray him, perhaps by trying to imprison him or strip him of his powers.
One plotline could be Naruto being transported to the Mandalorian universe. He has to learn the ways of the Mandalorians while still relying on his ninja skills. Another could be a Mandalorian coming to the Naruto world and Naruto teaming up with him, sharing their combat knowledge. For example, Naruto could teach the Mandalorian about chakra, and the Mandalorian could teach Naruto about their advanced weaponry.
Perhaps in this fanfic, Naruto is forced to make a choice between his ninja values and the Jedi code. He might choose something that the Jedi don't agree with, like using his chakra in a way that goes against their light - side - only beliefs. The Jedi then shun him, making Naruto feel betrayed. He might then try to find his own path, separate from both the ninja world and the Jedi order.
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.
Well, a possible plotline is that Naruto has to deal with the fact that he has the power of the Kyuubi in a more innate way. Maybe he discovers that he can access certain abilities that are unique to being the son of Kyuubi, like a deeper connection to the chakra of the nine - tailed beast. There could also be a plotline where the Akatsuki target him not just for the Kyuubi's power but because of his special connection to it as its son. And his own village might have to decide whether to protect him or sacrifice him for the greater good.
One plotline could be that Naruto finds Zangetsu during a mission in a hidden part of the ninja world. He then has to keep it a secret from his village while he tries to figure out how to use it. Another could be that an enemy uses some sort of dark magic to force Zangetsu onto Naruto, and he has to learn to control it to break free from the enemy's control.
Maybe a group of villains in the RWBY fanfiction are trying to summon Dark Naruto to use his power for their own evil purposes. The RWBY heroes find out about this plan and have to stop the summoning. Along the way, they meet some characters from the Naruto universe who are also trying to prevent the misuse of Dark Naruto's power.
One potential plotline could be Naruto being summoned to the world of Rias by accident. He then has to figure out how to get back home while also getting involved in the power struggles within the devil world. Maybe he becomes a key player in a battle for control of a certain territory.
Well, perhaps the Jedi, in the Naruto fanfic, is betrayed because he refuses to use his powers in a way that the hidden village wants. For example, they might want him to use the Force to assassinate an enemy leader. When he refuses, they spread false rumors about him being a spy from another land. As a result, he has to team up with some outcast ninjas who believe in his innocence and together they fight against the unjust accusations.
The Jedi Council themselves could be the main antagonists. Since they are the ones betraying Naruto, they would be the ones he has to oppose. Their actions of betrayal would drive the conflict in the story.