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.
There's a chance that the main antagonist is a former member of Fairy Tail who was banished for some dark deeds. When Natsu joins, this person sees it as an opportunity to return and take over the guild. They know a lot about Fairy Tail's secrets and weaknesses, and they use this knowledge to their advantage. They might also have formed alliances with other dark guilds in their time away from Fairy Tail.
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.
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.
One possible plot could be that Natsu has been living a different life away from Fairy Tail. Maybe he was raised by another guild unknowingly. When he finally joins Fairy Tail later, he has to prove himself to the existing members who are skeptical of his late arrival. He might have unique magic skills he developed elsewhere that surprise everyone.
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.
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.
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.
There might be a group of anti - magic fanatics as the main antagonists. They view Natsu's new and extremely powerful magic as a danger to the natural order of the magical world. They would try to eliminate Natsu and any other powerful mages in Fairy Tail who support him, believing that magic should be limited and controlled, not allowed to reach such overpowered levels as Natsu has.
A powerful dark wizard who has a vendetta against Natsu. Maybe he blames Natsu for something that happened in the past, like the destruction of his dark guild by Fairy Tail. So, when Natsu and Happy leave Fairy Tail, he sees it as an opportunity to get revenge.
Another option could be a dark wizard from the past who was once defeated by the founders of Fairy Tail. But Natsu's time - traveling causes some sort of ripple effect that brings this wizard back to power. He then wants to take revenge on the guild and sees Natsu as a symbol of the future that he wants to destroy.