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.
The main antagonist could be the evil Naruto himself. Since he has turned to the dark side, his actions and motives would be against the well - being of the village and those around him, including Kushina. He might be the source of conflict and chaos.
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.
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 characters are Naruto, who is in a rather tragic situation with his godlike abilities yet being abandoned. And Kushina, whose actions of abandonment drive the story forward. There might also be other characters like Naruto's friends or other ninja from the village who could play roles in how Naruto copes with the abandonment and his journey with his powers.
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.
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.
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.