Maybe a powerful and corrupted Pokemon that has gained sentience and wants to rule both the Pokemon world and Naruto's world. It sees Naruto as an obstacle because of his godlike powers. This Pokemon could have the ability to control other Pokemon and use them to attack Naruto and those who oppose it. It would be a major antagonist as Naruto has to find a way to defeat it and restore peace to both worlds.
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.
Maybe there's a rogue ninja who has developed a new and dangerous jutsu that can counter Naruto's powers. This ninja wants to prove himself as the strongest by defeating Naruto and taking over the bijuu's power. He might be jealous of Naruto's newfound status and the respect he gets from the other ninjas.
It could be a group of rogue ninjas who want to steal Naruto's godlike powers for themselves. They might be led by a powerful and evil ninja who has his own motives for wanting such power.
Maybe an ancient evil that has been awakened. This entity is so powerful that it takes the combined godlike powers of Naruto and Kushina to stand against it. The antagonist could have some connection to the origin of chakra or an old, forgotten curse.
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.
There might be some ancient forces or entities that are awakened by Naruto and Sasuke's new 'godlike' status. These could be demons or spirits that were sealed long ago and now see Naruto and Sasuke as threats to their plans of domination. They would be very powerful and require Naruto and Sasuke to use all of their enhanced abilities to defeat.
Maybe a group of outcast shinobi who are jealous of Naruto's power and Hanabi's connection to the Hyuga clan. They band together to try and take over the village, and Naruto and Hanabi have to stop them. Their leader could be a former Leaf Village ninja who was wronged in the past and now wants revenge.
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.