It could be because of a power struggle. Suppose Naruto discovers a new, extremely powerful power within himself, but the village elders or some members of Team 7 are afraid of it. They try to suppress him. Feeling cornered and betrayed first, Naruto could then turn against them. He might believe that he has to protect this new power and use it for what he thinks is right, even if it means going against his old team.
One reason could be some sort of betrayal he feels. Maybe he discovers a secret that makes him think Team 7 was never truly his team. For example, if he found out that the village leaders had some ulterior motives for forming the team that involved using him.
In some fanfictions, Percy might betray Natasha due to his own ambition. He could see an opportunity to gain more power or status by siding against her. For example, if there's a power struggle within their group or world, and he thinks that by betraying Natasha, he can get on the winning side and be rewarded. It could also be a case of jealousy. If Natasha has always been in the spotlight or has more skills and abilities, Percy might feel overshadowed and his jealousy could lead to betrayal.
It could also be due to some external influence. Perhaps an evil organization has manipulated Ash in some way, forcing him to act against Alola. They might have used mind control or blackmailed him with something he holds dear, like the safety of his Pokémon.
Perhaps Natsu feels betrayed by the guild first. There could be a situation where he believes the guild has turned its back on one of his closest friends or on a principle he holds dear. This sense of being let down by the guild might lead him to take extreme actions that seem like betrayal. It could also be related to a power struggle. If there's a new power within the guild that Natsu sees as a threat to the guild's original values, he might try to oppose it in a way that looks like betrayal from the outside.
One possible reason could be jealousy. Maybe some members of Team 7 are jealous of Naruto's natural talent that he doesn't even realize he has. Another reason might be a misunderstanding. Naruto is often brash and loud, and his teammates could misinterpret this as him being over - confident or show - offish, when in reality he's just trying to prove himself. Also, there could be a pre - existing bias. If some members of Team 7 come from more 'privileged' ninja families, they might look down on Naruto who was an outcast in the village for a long time.
Well, in a fanfiction context, it could be possible if we consider a crossover universe where Naruto somehow ends up in the Star Wars galaxy. Maybe he's brainwashed by the dark side's influence which is similar to some dark forces in his own world. This could lead him to betray the Jedi ideals that he might have adopted during his time there.
One possible plotline could be that Naruto is somehow transported to the MLP world. He might be tricked into believing the ponies are a threat and thus 'betray' them by taking actions against them. For example, he could be misled by a dark magic user in that world who convinces him the ponies are hoarding power that could be dangerous.
One possible reason could be a misunderstanding. Maybe they were misled by false information or an enemy's trickery that made them think Naruto was a threat at that moment. Another reason might be extreme pressure or a life - or - death situation where they thought sacrificing Naruto was the only way to save the rest of the team or complete a crucial mission.
One possible reason could be a sense of being undervalued. Maybe he felt that his teammates didn't fully appreciate his efforts during the Wave mission. For example, if Sasuke got most of the credit, Naruto might feel pushed aside.
In some fanfictions, Arceus might be bound by some ancient rules that Ash unknowingly breaks. These rules are so important to Arceus that it feels compelled to betray Ash. For example, if there's a rule about not interfering with a certain type of Pokémon evolution and Ash does it accidentally, Arceus could see it as a major transgression and take action against him.