A powerful demon from another dimension could be the main villain. This demon has noticed Natsu's growing power and sees him as a threat. The demon has the ability to create illusions and false memories, which could be used to drive a wedge between Natsu and the Fairy Tail guild. He works in secret, slowly weakening Natsu's mental state before making a big move.
There could be a traitor within the Fairy Tail guild itself who becomes the main villain in Natsu's secret fanfiction. This person has always been jealous of Natsu's popularity and power. They secretly make deals with outside forces to bring down Natsu. They spread false rumors and cause chaos within the guild, all while pretending to be Natsu's friend. This would make for a very interesting and complex villain in the story.
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.
Perhaps an old enemy of Fairy Tail who sees Natsu as a new threat. They might target Natsu specifically to prevent him from strengthening the guild. This antagonist could have a long - standing grudge against Fairy Tail and see Natsu as the new hope for the guild, so they try to eliminate him before he can fully join.
Perhaps the secret is that Lucy has a unique magical item that is very powerful and dangerous. Natsu keeps it a secret because he doesn't want other mages in Fairy Tail to get greedy or misuse it. This item could be something that was passed down in Lucy's family and she doesn't fully understand its potential yet.
It could be a powerful wizard who has a grudge against Fairy Tail and sees Natsu as a new threat. This wizard might have been secretly observing Fairy Tail for a long time and when Natsu joins, they decide to strike. Their magic could be something unique like shadow manipulation or time - based spells.
It could be a dark wizard who has a grudge against Fairy Tail. This wizard might be the one who made Natsu lost in the first place, by using some devious magic to separate him from his guild.
It could be a rival wizard from another guild. This wizard might be jealous of Natsu's power and popularity within Fairy Tail. So, they fabricate evidence to get Natsu expelled, aiming to not only remove him as a competitor but also to create chaos within Fairy Tail. They could continue to be a thorn in Natsu's side as he tries to clear his name and get back to the guild.
One possible antagonist could be a dark wizard from a rival guild who is jealous of Natsu's status as an alpha in Fairy Tail. This wizard might try to undermine Natsu's leadership and the guild's reputation.
It could be a powerful dark wizard who has a grudge against Fairy Tail. This wizard might see Natsu and Mirajane's joining as an opportunity to strike at the guild when it's in a state of flux. He could be someone who was once defeated by Fairy Tail in the past and has spent years building up his power for revenge.
It could be a rogue dragon slayer. Someone who has turned against the ways of dragon slayers and wants to destroy Fairy Tail for some personal vendetta against Natsu or the guild as a whole.
The Fairy Tail guild members who supported Natsu's exile could be antagonists. They might believe in false accusations against him or have their own motives for wanting him out of the guild, like jealousy of his power or popularity.