In some fanfictions, it could be that Harry discovers a dark secret about the wizarding world that his friends don't believe or are too afraid to accept. His friends, thinking he has gone mad, side with the established order. They then betray Harry by reporting his so - called 'crazy ideas' to the Ministry of Magic, leading to Harry being hunted.
Well, perhaps in the fanfiction, it shows that Harry's parents made a deal with Voldemort before their deaths. They promised to hand Harry over in exchange for something, like power or protection for themselves. But then things went wrong and they ended up dying, still leaving Harry feeling betrayed as he discovers this truth later. It could also be that his parents were actually working against the Order of the Phoenix all along and Harry was just a pawn in their real plan.
A common plot is the misinterpretation of Harry's actions. His friends might think he's being secretive about something dangerous, like a new form of magic he's discovered, when in fact he's just trying to protect them. Another plot could be that a new character enters the story and manipulates his friends against Harry for their own gain.
One possible plot could be that Naruto discovers his friends have been secretly working with an enemy. They might have been promised power or something valuable in return for betraying Naruto. Maybe they spread false rumors about Naruto, turning the village against him.
Well, usually in such fanfictions, Harry might face a lot of emotional turmoil and have to find his way alone to overcome the betrayal and the challenges that come with it.
One possible plot could be that Fleur betrays Harry in a Triwizard Tournament - related task, perhaps by secretly helping the other champions. Another might be that Harry discovers Fleur has been passing information about the Order of the Phoenix to the wrong side. Maybe Fleur betrays Harry's trust regarding a personal secret, like his feelings for Ginny, and uses it to her advantage in some way.
One possible plot could be that everyone believes false rumors about Harry being a dark wizard. His friends from Hogwarts, including Ron and Hermione, turn their backs on him. Harry then has to find a way to prove his innocence all alone, perhaps by going into hiding and secretly investigating who spread the lies.
Well, one reason could be jealousy. Maybe his friends envy his fame or special abilities. Another could be misinformation. If they are fed false information about Harry, they might turn against him. For example, if someone convinces them that Harry is secretly working for the enemy.
In some fanfictions, it could be a misunderstanding that spirals out of control. Hermione and Ron misinterpret one of Harry's actions. For instance, Harry might be trying to protect them in a secret way, but it looks like he's up to something bad. Their lack of trust then grows, and they end up betraying Harry, perhaps by not coming to his aid when he really needs them, which could have serious consequences for Harry.
The Ministry of Magic could also be the main antagonist in this case. If the Ministry is corrupted or under the influence of dark forces, they could manipulate Harry's friends. They might convince his friends that Harry is a danger to the wizarding world order, and his friends, being naive or misinformed, end up betraying him.
One common plot is Percy being framed by his friends for a crime he didn't commit. This often leads to him being hunted by other demigods or facing exile. Another is his friends siding with his enemies for power or personal gain, leaving Percy alone to fight against the odds.