One likely antagonist could be those who fear Naruto's new power. For example, some of the traditional shinobi clans who are used to being in power might see Naruto as a threat. Another could be ancient evil forces that were sealed away long ago and now sense Naruto's god - like power as a way to break free. They might try to either corrupt Naruto or destroy him to prevent him from stopping their plans.
In the 'naruto ascends to godhood fanfiction', antagonists could be diverse. There might be a group of rogue shinobi who believe that Naruto's ascension to godhood goes against the natural order of the ninja world. They would band together to try and take him down. Additionally, there could be interdimensional beings who view Naruto's new power as a threat to their own existence or their plans for other dimensions. These beings would use their own unique powers and strategies to oppose Naruto.
Often, ancient and powerful demons or dark gods can be antagonists. They might see Naruto's newfound godhood as a threat to their own power or plans. For example, a demon that has been sealed away for centuries could be awakened by Naruto's ascension and seek to destroy him.
Well, in such a fanfiction, Naruto might gain incredible powers that are god - like. He could probably control elements on a whole new level, like creating massive tsunamis or volcanic eruptions with a simple thought. Maybe he'd also have the ability to manipulate life and death, bringing back the dead or preventing someone from dying. It would be a really exciting story to read as Naruto would be way more powerful than in the original series.
Hermione would likely be a main character. She might be the one who tries to guide Harry in using his new powers wisely. Ron could also be there, perhaps being a bit in awe of Harry's new status but still being his loyal friend. Dumbledore might also play a role, even if it's from beyond the grave. His wisdom could be a guiding force for Harry as he navigates his god - like existence.
Perhaps some rogue ninja from other villages. They might see Naruto as a symbol of Konoha's power and want to take him down to weaken Konoha. These rogue ninjas could be led by a powerful and vengeful shinobi who has a grudge against Konoha. So when Naruto is alone on a mission or something, they attack, and that's when Minato steps in to save him.
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.
There could be internal antagonists within Naruto's own village. Some of the more conservative ninja in the village might not trust Naruto's new - found skills and powers obtained from Zetsu. They could try to undermine Naruto or even attempt to exile him, fearing that he has been corrupted by Zetsu's teachings.
The Akatsuki could still be the main antagonists. Since Naruto is being trained by Shisui, they would see Naruto as an even greater threat. His new skills under Shisui's training could put their plans at risk. For example, if Naruto becomes better at stealth and infiltration, he could disrupt their operations more effectively.
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 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.
The village elders could be antagonists. They might see Naruto and Kakashi as threats to their traditional way of ruling the village and use false accusations to banish them.