A new and powerful dark ninja could be created as the main antagonist. This ninja could have a vendetta against Minato and see Naruto as an easy target to get to Minato. He might possess some dark and forbidden jutsu that even Minato has trouble countering. This would put Naruto in a difficult situation as he has to protect the village and his master while still learning and growing as a ninja. Additionally, there could be an ancient evil force awakened by Naruto's growing power under Minato's training, which wants to destroy the ninja world starting with the Hidden Leaf.
The Akatsuki could still be the main antagonists. However, in this fanfiction, they might target Naruto earlier because they know Minato is training him. They could fear that Naruto would become an even greater threat to their plans in the future. Pain, in particular, might see Naruto as a symbol of the Hidden Leaf's strength that needs to be eliminated. Also, there could be an internal antagonist within the Hidden Leaf, someone who is jealous of Naruto's special relationship with Minato and tries to undermine him.
Well, one antagonist could be Sasuke. If he goes down a dark path again, his actions could cause Naruto great pain. Minato would then watch as Naruto tries to deal with his best friend's betrayal or attacks. Zetsu is also a potential antagonist. He has his own hidden agendas and could be manipulating events behind the scenes to make Naruto suffer. And there are always the hidden threats within the shinobi world, like certain hidden village leaders who might see Naruto as a threat and try to harm him, with Minato observing all this.
One possible plot could be Naruto learning unique jutsu from Minato right from the start. Minato could teach Naruto how to use the Flying Thunder God Technique at an early age. This would change Naruto's battles significantly, as he could quickly move around the battlefield and surprise his enemies. He might also learn about Minato's leadership skills and how to handle difficult situations within the village, making him more respected among the villagers much earlier in the story.
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.
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.
The Sound Ninjas could be great antagonists. They could use their own unique parkour - like skills to try and stop Naruto. They might be chasing him through the forest, and Naruto has to use his parkour skills to outmaneuver them.
Maybe some corrupt officials within the prison system itself. They oppose Naruto's more humane and reform - focused approach to prison management. They might try to undermine him at every turn, for example, by cutting off resources or spreading false rumors about him among the prisoners.
Maybe a group of dark - type Pokémon that have banded together and are trying to overthrow Arceus. They view Naruto as an easy target at first, but quickly realize he is a formidable opponent with his ninja skills and new Pokémon - related powers. They would constantly try to undermine Naruto and his efforts to protect the Pokémon world.
It could be Danzo. He might have some hidden motives and manipulate situations to make Naruto look like a threat, forcing Minato to arrest him.
Perhaps an ancient evil that was sealed away long ago is awakened when Minato is revived. This entity could be a powerful demon or a dark ninja from the past. It wants to destroy the ninja world and Minato stands in its way. Minato, with his skills and knowledge, has to figure out how to defeat this ancient evil with the help of Naruto and the other Leaf Village ninjas.
Perhaps a new and original antagonist could be created for this fanfiction. This antagonist could be a rogue ninja who has mastered a forbidden jutsu that allows him to manipulate time as well. He could be the one who sets up the events that lead to Minato's endangerment, and Naruto has to figure out his motives and stop him while also saving Minato.