Gray might be the main antagonist in this type of fanfiction. Gray has a cool exterior but can be quite stubborn. He might bully Naruto because he doesn't like the idea of someone from a different world coming into their territory and getting so much attention. He could use his ice - make magic to play cruel tricks on Naruto, like freezing his feet when he's trying to run away from the bullies.
It could be Natsu. He's hot - headed and might not understand Naruto's ways at first. He could see Naruto as a threat to his position in the Fairy Tail guild and start bullying him to assert his dominance.
The main antagonist could be a powerful demon that has been sealed in the Fairy Tail world for a long time. Naruto's arrival disrupts the seal somehow, and the demon sees Naruto as a key to fully breaking free. The Fairy Tail members and Naruto must put aside their differences and combine their powers to fight this demon.
It could be a dark wizard from the Fairy Tail world who sees Naruto as a threat because of his unique powers. This wizard might try to stop Naruto from leaving, fearing that he'll take the knowledge of Fairy Tail's magic to other places.
Maybe the main antagonist is an outside force that has influenced the Fairy Tail guild to exile Naruto. For example, a dark guild could spread false rumors about Naruto, making the Fairy Tail members believe that he is a danger to them. This way, they can get Naruto out of the picture and then plan an attack on the Fairy Tail guild without having to deal with Naruto's power.
It could be an evil mage from Fairy Tail who sees Naruto as an outsider and a threat to the balance of power in the magic world. This mage might try to use Naruto's neglected past against him, trying to manipulate him into doing bad things.
It could be a former Fairy Tail member who turned to the gangster life. They know all the guild's secrets and weaknesses, so they can be a very formidable opponent. They might have left the guild because they felt betrayed or didn't get the recognition they thought they deserved.
It could be an ancient dragon that has been awakened from a long slumber. This dragon might have a vendetta against Ignia or the Fairy Tail guild for some past transgression.
Well, perhaps in this fanfiction, Fairy Tail characters bully Naruto because they are jealous of the attention he gets from certain characters in their shared universe. They start by making fun of his appearance, like his orange jumpsuit, and then escalate to more mean - spirited pranks, like using their magic to disrupt his ninja training.
It could be a jealous Fairy Tail member. Maybe someone who is envious of Naruto's unique powers and the attention he gets from some of the guild members. This person could start spreading lies about Naruto to turn the others against him.
A group of rogue mages who oppose the idea of Yukino joining Fairy Tail. They might view Fairy Tail as a threat to their own plans in the magical world. They target Yukino as the 'newcomer' in the guild, thinking that if they can get rid of her, they can weaken Fairy Tail. They use various underhanded tactics like spreading false rumors about Yukino within the guild and attacking her when she is on solo missions.
It could be Zeref. Since he has a complex relationship with Natsu in the original story, he might manipulate things behind the scenes to make the Fairy Tail guild betray Natsu. Maybe he wants to isolate Natsu for his own evil plans.