Well, in this fanfiction, the Akatsuki could be the main antagonists. They would view Naruto's godlike powers as a major threat to their goals. Since Naruto has been trained by Shendu, his abilities would be unpredictable and extremely powerful. They might band together to try and take Naruto down. Additionally, there could be some ancient demons or spirits that are awakened by Naruto's new powers and they see him as an intruder in their realm, so they become antagonists as well. They would use their own dark magic and powers to oppose Naruto.
The main antagonists could be a group of rogue ninja who are envious of Naruto's powers. They might form an alliance with some of the more power - hungry characters in the Naruto universe, like Kabuto. Another potential antagonist could be an old enemy of Shendu who decides to target Naruto as a way to get back at Shendu. This enemy could have powers that are equal or even greater than Naruto's new godlike abilities, and would stop at nothing to defeat him. Also, some of the ninja villages that fear Naruto's power might turn against him, making them antagonists in the story.
It could be the other Hidden Villages. Since Naruto is becoming so powerful under Danzo's training, they might see him as a threat and try to stop him. Maybe they would send their best ninjas to take him down.
In such a fanfiction, Naruto could gain unique powers. Shendu, being a powerful and often devious entity, might train Naruto in unorthodox ways. Naruto could learn new combat styles and perhaps some dark or ancient techniques. This would likely put him at odds with his usual ninja values at first, but he'd probably find a way to blend the new knowledge with his own beliefs to become an even more formidable shinobi.
The Akatsuki could still be the main antagonists. Even with Naruto being trained by Minato and becoming godlike, the Akatsuki's goals of collecting the tailed beasts would put them in direct conflict with Naruto. Their powerful members, like Pain or Itachi, would pose a great challenge to Naruto, despite his new skills.
One potential antagonist could be those who fear Naruto's new - found godlike powers. There might be ninja from other villages who see Naruto as a threat to the balance of power. Another could be remnants of Kaguya's old enemies who resurface, seeing Naruto as a continuation of Kaguya's influence and wanting to stop him. Also, there could be dark forces within the ninja world that want to corrupt Naruto's new powers for their own evil purposes.
Perhaps there are dark forces from another dimension. These forces might be attracted to Naruto's power and want to either steal it or destroy him to prevent him from using it against them. They could be powerful demons or sorcerers with their own motives.
Another possibility is that the main antagonists could be the leaders of the other ninja villages. They might view Naruto's godlike and rogue status as a danger to the balance of power among the villages. So, they could form an alliance against Naruto, leading to a lot of political intrigue and conflict in the story.
The main antagonists could also be a group of rogue ninjas who have made a pact with some meta - humans from the Flash's world. They could be after Naruto because they want to use his connection to Barry Allen to gain access to the Speed Force. These antagonists would be a combination of the stealth and trickery of ninjas and the super - powers of meta - humans. They could create a lot of chaos in both the Naruto and Flash worlds, forcing Naruto to use all of his newly acquired skills and powers to stop them.
It could be his own family members who abandoned him. They might come back as antagonists, trying to stop Naruto from reaching his full potential or causing trouble for him out of envy or regret. Maybe they have joined a dark force and are now working against him.
In this fanfiction, the main antagonists might be a group of dark chakra - users. They are jealous of Naruto's godlike powers and want to take over the empire for their own evil purposes. They could be using dark magic to corrupt some of the people in the empire, turning them against Naruto. There might also be some power - hungry politicians within the empire who are not satisfied with Naruto's leadership and want to seize power for themselves. They would plot behind the scenes to bring down Naruto and take over the reins of the empire.
Maybe it could be other ninja clans who are jealous of Naruto's newfound sword bloodline. They might see it as a threat to their own power and status in the ninja world.