The dark guilds would be great antagonists. They might see Natsu's new leadership as a threat and try to undermine his guild. They could send their best mages to disrupt the guild's operations and steal important magical artifacts.
There could be a powerful, ancient magical being that has awakened and views the guilds as a disturbance to the natural order of magic. As Natsu is the guild master, it focuses on his guild first. This being has abilities that are completely different from what the guild mages are used to, making it a formidable foe.
Perhaps a group of rogue mages who were once banished from other guilds. They hold a grudge against all guilds in general and target Natsu's guild specifically. They use underhanded tactics like spreading false rumors to create division within 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.
Maybe in the 'natsu guild master fanfic', Natsu becomes guild master during a time of crisis. A dark magic is spreading and threatening all the guilds. Natsu has to make difficult decisions, like forging alliances with former enemies. He uses his fiery determination to inspire his guild and they fight back the dark forces together. He also discovers new aspects of his magic along the way to better protect the guild.
Maybe an old enemy of Natsu's resurfaces. This enemy is jealous of Natsu's newfound happiness with Cana and tries to take Cana hostage to force Natsu to fight him. This would create a major conflict in the fanfiction.
It could be another guild that sees Natsu as a threat. They might find out about Lucy kidnapping Natsu and try to use the situation to their advantage. For example, they could try to steal Natsu's magic or get information out of him while he's in a vulnerable state. Another possible antagonist could be a character who has a grudge against Lucy. They might try to stop her from getting away with the kidnapping or use it as a way to get revenge on her.
The Titans related to water, like Oceanus, could be a great antagonist. He might be jealous of Percy's growing power over water and try to stop him.
A powerful dark wizard who was once a member of Fairy Tail but was banished for using forbidden magic could be a great antagonist. They hold a grudge against the guild and especially the guild master for their expulsion and now seek revenge by trying to destroy the guild from within.
A powerful dark guild could be the main antagonists. They might be jealous of the combined power of Natsu and Mirajane's family and seek to destroy them to gain more power in the magical world.
Maybe a rival guild that is jealous of Fairy Tail's new addition. They might think that having a baby with such strong magical potential in Fairy Tail gives them an unfair advantage. So they try to kidnap the baby to either keep it for themselves or use it to bargain with Fairy Tail.
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.
One possible antagonist could be a dark wizard who wants to control the sea for his own evil purposes. Maybe he plans to use the power of the ocean to spread his dark magic across the land. Another could be a sea pirate captain who is jealous of Natsu's power and tries to stop him at every turn. Or it could be a sea monster that has been corrupted by dark magic and sees Natsu as a threat.