A plot could involve the Leaf Village betraying Naruto when a powerful and ancient curse is placed on him that makes him seem like a mind - controlled puppet of a great evil. The village, in its panic, decides to take preemptive action against Naruto without fully investigating. This could lead to Naruto having to fight not only the external forces that are trying to use the situation to their advantage but also his own former comrades from the Leaf Village who are now hunting him down.
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 possibility is a false accusation. If Naruto is wrongly accused of a serious crime like treason or murder within the Leaf village, and no one believes his innocence, he might feel so betrayed that he turns against the village. Another factor could be a conflict of ideals. If the Leaf starts to pursue a path that Naruto believes is morally wrong, such as unjustly attacking another village, he could oppose the Leaf's actions to the point of betrayal.
One possible plotline could be that Akeno is forced to betray Naruto due to some external threat or blackmail. Maybe an enemy has something over her that she values greatly, like the safety of her friends or family in her own world. So, she has to act against Naruto to protect them.
A plotline might involve Naruto hearing rumors about a powerful artifact in Nakedesho village. He travels there to find it, but once he arrives, he realizes that the village is being threatened by a group of rogue ninjas who also want the artifact. Naruto then has to team up with the villagers to fend off the rogues and protect the artifact. Or perhaps Naruto stumbles upon the Nakedesho village while on a journey. He finds that the village is suffering from a famine due to a natural disaster. Naruto uses his knowledge and abilities to help the villagers rebuild and find new sources of food.
It could be due to a prophecy misinterpretation. Suppose there is a prophecy that Naruto misinterprets as the Leaf Village needing to be destroyed for the greater good. Or perhaps he is tricked by a very cunning enemy who convinces him that the Leaf Village is the root of all the problems in the ninja world.
The village might experience a huge boost in morale. Naruto killing Pain would be seen as a major victory, and the villagers would feel safer. They would look at Naruto as an even greater hero, which could lead to more trust and unity within the village.
Another plotline might be that Percy betrays God out of a sense of self - preservation. Suppose there's a great threat coming, and Percy believes that siding with an enemy of God is the only way to save himself or the world he cares about. He might think that God's power is not enough to protect them, and so he makes a deal with the other side, which is seen as a betrayal.
One possible plotline could be that Snape remains a loyal Death Eater throughout. He continues to carry out Voldemort's orders without question. Maybe he helps Voldemort in his search for more powerful dark magic, and in this version, he has no hidden motives of protecting Harry or the Order. He is fully committed to the Dark Lord's cause, which could lead to a much darker and more hopeless situation for the wizarding world.
One possible plotline could be that Ash is influenced by a powerful and evil force. This force convinces Ash that Cynthia is somehow a threat to his ultimate goal, like becoming the greatest Pokémon trainer. So, he betrays her by stealing a crucial Pokémon of hers during a big tournament. This would lead to a lot of drama and conflict as Cynthia would be shocked and heartbroken, and Ash would start to realize the error of his ways as the evil force begins to control him more.
One possible plotline could be that Percy is under some sort of mind control. Maybe a new villain has the power to manipulate his thoughts and actions, making him turn against Annabeth. For example, the villain could use Percy's insecurities about his past mistakes to drive a wedge between them. He might start by leaking some of Annabeth's secret plans to the enemy, causing her to be in danger without realizing Percy is the source.