Perhaps Harry discovers a dark secret about the side he has been fighting for. This discovery makes him feel betrayed and he turns to Tom thinking that Tom offers a different kind of solution. It could be that Tom presents himself as a reformed person or has a convincing argument about a new order in the wizarding world that Harry, in his disillusioned state, starts to believe. Then, the story could follow how Harry's relationships with his old friends deteriorate as he gets closer to Tom's side.
In this fanfiction, it might be that Harry is under the influence of a powerful mind - controlling spell by Tom or his followers. He doesn't realize he's being controlled at first. As he starts to join Tom, he begins to have strange dreams and visions. His friends notice the change in him but are unable to stop it right away. The story could then revolve around their attempts to break the spell and bring Harry back while Harry, under the influence, helps Tom carry out his evil plans.
One possible plotline could be that Harry betrays Draco in a duel. Maybe there was some sort of misunderstanding or a secret deal that Harry made with someone else that required him to turn on Draco during the duel. For example, if there was a dark wizard threatening Harry's friends and the only way to save them was to sacrifice Draco in the duel by using a forbidden spell against him.
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.
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 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.
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.
In this fanfiction, Naruto might join Madara because of some sort of time - travel or alternate reality situation. He could find himself in a world where Madara's actions seem more justifiable. Naruto, being Naruto, would still strive for peace. So he might try to guide Madara towards a more peaceful solution while being part of his group. This could create a really unique dynamic where Naruto is constantly trying to nudge Madara in the right direction while also dealing with the other members of the group who may not be as open to change.
A plotline could involve them going on adventures outside of the wizarding world. They could travel to different magical realms, encountering strange creatures and magic systems. Along the way, they learn more about each other's strengths and weaknesses. Harry might learn from Tom how to be more strategic, and Tom could learn from Harry about the importance of loyalty and friendship. Their friendship could be tested in these new and dangerous situations, but ultimately it could grow stronger.
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.
Perhaps in the fanfic, Ash betrays Tyson because of a misunderstanding. There could be a false rumor spread about Tyson being involved in some unethical Pokémon training methods. Ash, believing the rumor without fully investigating, turns his back on Tyson. Later, when he realizes the truth, he has to work hard to regain Tyson's trust.
One possible plotline could be that Naruto, heartbroken from a failed relationship or the loss of a dear friend, throws himself into the dangerous and secretive world of ANBU to numb his pain. He might start off as a reckless agent, but gradually find purpose in protecting the village in a more covert way. This could lead to him making new, deeper friendships within the ANBU ranks.