Perhaps in the fanfiction, Natsu is betrayed by someone he trusts in a mission. For example, they might leave him behind in a dangerous situation to fend for himself while they take the credit for the mission. Or it could be that a love interest betrays Natsu by choosing someone else over him due to some false perception or external pressure.
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.
It could be Gray. Although they are friends most of the time, in a fanfiction, there could be a plot twist where Gray's envy of Natsu's abilities gets the better of him, and he betrays Natsu. Maybe Gray thinks that by getting rid of Natsu, he can be the top mage in their guild.
One possible plot could be that Natsu gets hurt during a battle with a powerful dark mage. His friends then have to find a way to heal him while also dealing with the threat of the mage still being around. Maybe they search for a rare magical herb or seek help from a reclusive healer.
One possible plot could be that Tails is betrayed by a close friend who becomes jealous of his intelligence and skills. For example, Sonic might start to feel overshadowed by Tails and in a moment of weakness, turn against him. This could lead to Tails having to fend for himself and prove his worth all over again.
One possible scenario could be that Natsu is killed in a battle against a powerful and unexpected enemy. Maybe a new dark mage appears with powers that can overpower Natsu's fire magic.
Sometimes, it's just a way to shock the audience. Fanfiction authors often like to take risks and do unexpected things to their beloved characters. Torturing Natsu can be a very unexpected and extreme move that can leave a lasting impression on the readers, whether they like it or not.
One possible scenario could be that Natsu confesses his love to a character, perhaps Lucy, and she rejects him because she doesn't see him in that way. She might think of him only as a good friend. Another scenario could be that Natsu is rejected in a job or a quest application within the fanfiction world. Maybe the guild he wants to join or the person in charge of a certain task doesn't believe he has the skills or the right attitude.
One possible storyline could be that Natsu is wrongly accused of a crime within the Fairy Tail guild. Maybe some false evidence is planted against him, leading the guild members to turn their backs on him. Another could be that a powerful enemy manipulates the guild into believing Natsu is a threat, so they betray him. It might also be that there's a misunderstanding about Natsu's powers or intentions, causing the betrayal.
One possible plot could be that Boruto is betrayed by his friends due to a misunderstanding. For example, they might think he has turned to the dark side because of some false evidence planted by an enemy. Another could be that Boruto is betrayed by the village he loves. Maybe the village leaders suspect him of a crime he didn't commit and turn against him.
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.