Well, perhaps the OC was wrongly accused of stealing a powerful magic item from the guild. The other members turned against the OC without really listening to their side of the story. Then the OC, feeling betrayed, decides to leave Fairy Tail and seek revenge or prove their innocence on their own.
One possible reason could be a misunderstanding within the guild. Maybe someone spreads false rumors about Natsu, leading others to believe he's done something wrong. Another reason might be a power struggle. If there are those in Fairy Tail who envy Natsu's strength and popularity, they could plot against him to get him out of the way.
In some cases, it could be a combination of characters. For example, a group of older and more traditional Fairy Tail members who don't like the new and different ways of the OC. They work together to isolate the OC, making them feel betrayed. So, this group of conservative guild members could be seen as the antagonists.
Well, it could be that in this fanfic, Naruto is somehow transported to the Fairy Tail universe. And due to his different power set and origin, the Fairy Tail members misunderstand him and think he's a threat. Maybe they see his shadow clone jutsu as some sort of dark magic and turn against him.
It could also be a situation where Naruto has his own motives that conflict with Fairy Tail's goals. Perhaps he discovers a power within Fairy Tail that he thinks is too dangerous and decides to take it upon himself to stop it, even if it means turning against them. He might think he's doing the right thing in the long run, but Fairy Tail sees it as a betrayal.
Well, in fanfiction, anything can be twisted for the sake of creating drama. Maybe the author wanted to explore a really dark and unexpected scenario. The writer might have thought that by having Naruto betrayed in a Fairy Tail - related setting, it would attract readers who are into crossovers and angst. It could be due to some kind of power struggle or misinformation within the fictional world created in the fanfic.
One idea could be that your OC is a powerful mage with a unique magic ability, like the power to control time on a small scale. They join Fairy Tail and at first are an outcast because of their strange magic. But during a big battle against a dark guild, they use their time - control magic to freeze the enemy mages for a short while, allowing Fairy Tail to win. This earns them respect and they become an important part of the guild.
Maybe there is a misunderstanding. Since it's a crossover fanfiction, communication between the two different worlds' characters might be difficult. So, Naruto could be misjudged and betrayed because of false assumptions.
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 Natsu's nightmare is related to losing his friends. In the nightmare, he might see Fairy Tail being destroyed and his friends being hurt or disappearing. This could lead to him waking up in a panic and then being extra protective of his guildmates in the real world.
It could be that Natsu has some sort of falling - out with the members of Fairy Tail. Perhaps there was a misunderstanding during a big mission, and he decides he can't stay any longer. For example, if his actions were misinterpreted and the guild members blamed him for something that wasn't his fault. He might leave to prove his innocence elsewhere.