Maybe in the new time, there are powerful political figures who oppose Jiraiya's presence because they fear he'll disrupt the status quo. They could use their influence and resources to try and stop him from interfering in their world. Additionally, there could be a time - traveling villain from another era who has their own agenda and clashes with Jiraiya in the new timeline.
It could be a group of rogue ninjas from the new time period who see Jiraiya as a threat to their plans. Since he has different skills and knowledge, they might want to eliminate him.
There might be an ancient evil that was dormant in the original time of Jiraiya but has awakened in the new time he travels to. This entity could be a major antagonist as it tries to spread chaos and destruction. Jiraiya, with his sense of justice and ninja skills, would then have to find a way to stop it. Another possibility is that some of the local ninja clans in the new time might misunderstand Jiraiya's intentions and see him as an enemy, leading to conflicts with them.
In the Naruto world, it could be Orochimaru. He might be interested in Naruto's newfound Pokémon - related powers and try to capture him to experiment on him. Orochimaru is always after power, and Naruto's unique abilities could be very appealing to him.
Another possibility is that some rogue ninja who have a vendetta against Hanzo might target Naruto as a way to get back at Hanzo. They could see Naruto as Hanzo's weakness and try to harm or kidnap him, which would then lead to a series of battles and confrontations in the fanfiction.
The main antagonists could be the traditional enemies of Camelot like Morgana. She might see Merlin's act of adopting Mordred as a threat to her plans. Also, some of the knights or nobles in Camelot who are superstitious and believe Mordred is a danger just because of the prophecies could be antagonists. They might try to separate Merlin and Mordred or even harm Mordred.
One interesting concept could be how Jiraiya's character adapts to the new time period. He's used to his own era's ninja ways, so seeing him navigate a different time with different rules and technology would be cool.
The Sith could be great antagonists. If Boba Fett travels to a time when the Sith are in power, they would surely see him as an intruder or a potential threat. Their dark side powers and political manipulation would be a huge obstacle for Boba Fett.
The Death Eaters could still be the main antagonists. They might see Fenrir's new alliance with Harry as a threat. Since they once used Fenrir for their dark deeds, they don't want him to turn good and expose their secrets.
It could be a group of scientists who created the Bioraptor Riddick for some evil purposes. When they find out that Harry has adopted Riddick, they want to take him back to continue their experiments.
It could be Sally's ex - partner if there was a not - so - nice one. This person might want to take the daughter back out of spite or some wrong idea that Percy isn't a good enough caretaker.
One possible antagonist could be Sabretooth. He might see Wolverine's newfound fatherly relationship with Peter as a weakness and try to use Peter to get to Wolverine. Sabretooth could be jealous of the bond Wolverine is forming and want to destroy it.
The Ministry of Magic itself could be an antagonist. If they don't approve of Hermione's adoption due to her age or some bureaucratic reasons, they could try to take the baby away. They might think she's not fit to raise a child, which would create a lot of conflict in the story.