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.
Another plotline might involve Tom believing that Harry has some hidden power that he can extract or use for his own dark purposes. So, he kidnaps Harry to figure out how to access that power. This could lead to a series of attempts by Tom to break Harry's will and get him to reveal the secret. For example, he might put Harry in a magically sealed room and use various spells to try and force the information out of him. Harry, on the other hand, could be trying to resist and find a way to escape or signal for help.
Perhaps in the fanfiction, Harry adopts Tom Riddle when he's still a young boy at the orphanage. Harry then uses his own experiences of growing up without parents to bond with Tom. He teaches Tom about magic in a different way than Dumbledore did, focusing on the positive aspects of magic for good. This could lead to Tom not becoming the evil Voldemort we know.
One possible plotline could be a magical accident that leads to the pregnancy. Maybe a spell gone wrong during a battle or an experiment.
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.
One possible plotline could be that Lily is forced into betraying Snape due to some dark magic influence on her. Maybe she's under a spell that makes her give away Snape's secrets to his enemies. Another could be that she betrays him out of jealousy. Suppose Snape gets closer to someone else, and Lily, in a fit of envy, does something that seriously harms Snape. It could also be that Lily is misled by false information about Snape being involved in some really bad deeds, and without proper investigation, she believes it and betrays 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.