The Akatsuki as a whole can be antagonists in these fanfictions. They are a group of powerful and dangerous ninjas. Maybe they have a new plan that involves capturing or killing Jiraiya, and Naruto has to stop them. Itachi Uchiha could also be an antagonist in some cases. Although he has his own complex story, his loyalty to the Akatsuki might put him at odds with Naruto when it comes to saving Jiraiya.
Pain is often one of the main antagonists. Since in the original story, Pain was the one who ultimately killed Jiraiya. So in fanfictions where Naruto saves Jiraiya, Pain is a natural choice to be the bad guy. Another common antagonist could be Orochimaru. He had his own vendetta against Jiraiya and the Hidden Leaf Village. He might be trying to use Jiraiya for some evil experiment or to gain access to the secrets of the Sage Mode.
Some fanfictions might feature rogue ninja as antagonists. These rogue ninja are after the bounty on Naruto's head or they are trying to steal Jiraiya's knowledge. They attack Naruto and Jiraiya during their travels, making it difficult for them to reach their destination.
One possible antagonist could be a rogue ninja from another village. They might target Tenten for her unique weapon - handling skills, thinking they can use her to create powerful weapons for themselves. Naruto would then have to face this ninja to save Tenten.
It could be some rogue ninja clans that are after Karin for her special abilities. They might see her as a tool to gain power or information. For instance, a clan that specializes in blood - related jutsu might want to use Karin's unique blood - sensing ability for their own evil purposes.
One potential antagonist could be a power - hungry shinobi from another village. They might view Hayate as a threat to their plans, maybe because Hayate is involved in some sort of peace - keeping mission between villages. So, they try to eliminate him. And Naruto, being the defender of his comrades, will not stand by and let that happen. There could also be a group of missing - ninjas who band together to take on Hayate, thinking he's an easy prey, but they underestimate Naruto's loyalty and strength.
In this fanfiction, it's possible that an ancient and powerful beast is the antagonist. The beast might have captured Pyraa to lure Naruto into a trap. Naruto will need to use all of his skills, including his Sage Mode if necessary, to defeat this beast and save Pyraa.
It could be some dark magic users from Lucy's world who see her as a threat. They might be trying to stop her from using her magic for good.
Maybe some new rogue ninja group that has a vendetta against the Uzumaki family. They see Boruto as a way to strike at Naruto, so they try to harm him, which then leads to Naruto having to save him.
The Akatsuki as a whole could be antagonists. In fanfictions, the Akatsuki might be interested in the power of Naruto's Evil Rinnegan. They could try to capture him to extract the power or use him in some way for their own goals. Pain, being a powerful member of the Akatsuki, could also be a specific antagonist. His own ideology about pain and peace might clash with Naruto's new, potentially more chaotic state with the Evil Rinnegan. Additionally, new original antagonists created specifically for the fanfiction could be common. These could be dark, powerful figures who are drawn to the power of the Evil Rinnegan and want to either possess it or destroy Naruto to prevent its misuse.
One possibility for the antagonists could be a rogue group of ninjas who are after the power of the Sound Four. They might see the Sound Four as a means to gain more influence in the ninja world.
One possible antagonist could be the Akatsuki members. They are always looking for strong opponents or valuable information. Maybe they target Iruka because they think he has some knowledge about Naruto that they can use, and Kakashi has to stop them.