Perhaps in the fanfiction, Naruto is betrayed when he discovers some dark secrets about the Western side. They might be involved in unethical experiments using ninja powers, and when Naruto tries to expose them, they turn on him. This would lead to a conflict where Naruto has to fight against the Western forces who were once his allies.
One possibility could be that Naruto is betrayed by the Western forces in the story because of a misunderstanding. Maybe they misinterpret his actions as being a threat to their own interests. For example, if Naruto tries to bring some new ninja techniques to the Western world for the sake of peace and cooperation, but they see it as an attempt to gain power over them.
At first, Naruto might try to reason with the Western side. He would want to understand why they betrayed him. He believes in the good in people, so he would hope that there was some misunderstanding. However, if they continued to be hostile, Naruto would become determined. He would gather his own allies, like his friends from Konoha, and form a resistance against the Western forces. He would use his powerful jutsus and his unwavering spirit to take on those who wronged him.
Maybe in this fanfiction, there are some artifacts or powers that both Naruto and Erza are after. Erza betrays Naruto to get her hands on this power first. This could set off a chain of events where Naruto has to find a way to stop her from misusing the power. It could also make Naruto question his own judgment in trusting her in the first place.
One possible plot could be that the gods, seeing Naruto's growing power as a threat, decide to turn the world against him. They might manipulate events to make it seem like Naruto has committed unforgivable crimes. For example, they could cause false memories in people's minds. Naruto would then have to fight not only against the physical enemies but also against the false accusations and the loss of trust from his friends.
Well, one possibility could be that Mavis has some sort of hidden agenda. Maybe she's being controlled by a greater evil force that makes her turn on Naruto. It could also be a misunderstanding. For example, false information is spread about Naruto, and Mavis believes it without proper investigation. Another idea is that Mavis has a different view of the ninja world compared to Naruto, and their conflicting ideologies lead to her betraying him.
Well, it could be that Naruto discovers the gods have been using him all along for some dark purpose, like to start a war between different ninja clans. Maybe they promised him power in the beginning but then turned on him when he started to question their motives.
One possible plot could be that Team 7 is manipulated by a powerful enemy. Maybe Orochimaru manages to cast a powerful genjutsu on them, making them believe Naruto has turned evil. So they turn against him. It could also be that they are forced to choose between Naruto and the safety of the village in some extreme situation and they wrongly choose to sacrifice Naruto.
In a 'Naruto betrayed harem fanfiction', it could be that Naruto is blamed for something he didn't do within the harem. For example, a valuable item goes missing and the harem members quickly point fingers at Naruto. They don't believe his innocence and start to shun him. Naruto then realizes that these people he thought were his friends in the harem are not so trustworthy after all, and thus he experiences betrayal.
Perhaps Hiruzen is being influenced by some dark force or a hidden group within the village. They convince him that Naruto, with the Nine - Tails inside him, is too dangerous to be left unchecked. So, Hiruzen, in a moment of weakness, decides to betray Naruto. He could secretly arrange for Naruto to be sent on dangerous missions alone with the intention of getting him killed. Naruto, being oblivious to this at first, later realizes what's going on and has to fight not only against external enemies but also against the betrayal of his own village leader.
One possible plot could be that Naruto, with his godlike powers, is betrayed by the village he once swore to protect. Maybe the villagers grow jealous of his strength and start to spread false rumors about him being a threat. As a result, Naruto, feeling hurt and betrayed, decides to leave the village and embark on a journey alone, facing new challenges and enemies outside the familiar setting of the Hidden Leaf.
Well, it could be that in this fanfiction, Naruto is given a mission that goes against the interests of the Sekirei. He might have to choose between his loyalty to his original world and the new relationships he has formed with the Sekirei. If he chooses his old world, the Sekirei could see it as a betrayal.