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.
In this fanfiction, perhaps there's a power struggle. Naruto, being a powerful ninja, could be seen as a threat to the RWBY world's power balance. So, the RWBY characters, out of fear or a sense of self - preservation, betray him. They might think he'll disrupt their way of life or take over their territory.
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.
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 Kurenai is somehow deceived into believing Naruto has done something really bad. Maybe she's tricked by an enemy who fakes evidence against Naruto. So, in her misunderstanding, she turns against him.
In this fanfiction scenario, perhaps Mirajane has her own dark secrets or hidden motives that lead to her betraying Naruto. She might be seeking power and sees Naruto as an obstacle. Or, it could be related to loyalty to her own guild or group. If there are conflicting interests between Naruto's world and her world, she might choose to side against Naruto to protect her own people.
Well, it could be that they betray their village. Maybe they are tricked into believing false information about Konoha being corrupt. So they side with an enemy force, thinking they are doing the right thing.
Well, one possibility is that Naruto is framed for a serious crime he didn't commit. Maybe someone fakes evidence that he's been working with the enemies of the village. His friends, believing the false evidence, turn their backs on him. He then has to fight not only against the village's distrust but also to clear his name and find out who really set him up.
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.
In a Naruto Lucifuge betrayed fanfiction, the betrayal could be part of a much larger conspiracy. Lucifuge might be under the control of a powerful dark force. He betrays Naruto not out of his own will, but because he is being manipulated. This could lead to a journey for Naruto to not only stop Lucifuge but also to find a way to free him from the control of this dark force. Naruto would have to face his own feelings of trust and friendship being broken while also trying to save his friend from the clutches of evil.
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.