Well, in this kind of fanfiction, there could be antagonists from other dimensions. Since Naruto is becoming godlike, his presence might disrupt the balance of other realms. Beings from those realms could come to the ninja world to oppose Naruto. Additionally, there could be ninja within Naruto's own village who are jealous of his rapid progress under Kaguya's training. They might secretly plot against him, trying to undermine his new powers and status. And then, there are always the age - old enemies of the ninja world, like the Akatsuki, or new organizations formed with the goal of taking over the world. They would surely see Naruto as a major obstacle and try to eliminate him.
Potential antagonists could include power - hungry warlords who want to harness Naruto's godlike abilities for their own rule. They might send their most skilled assassins or warriors after Naruto. There could also be ancient evils that were once sealed away but are now awakened by Naruto's new power. These could be dark spirits or demons that have a vendetta against Kaguya and by extension, Naruto. Moreover, some of the shinobi clans that have long - standing rivalries with Konoha might view Naruto's rise as an opportunity to finally take down Konoha. They would ally with any force that opposes Naruto and try to bring about his downfall.
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.
The Otsutsuki clan members other than Kaguya could be antagonists. Since Kaguya is training Naruto, they might see Naruto as a threat to their plans.
Perhaps Orochimaru could still be an antagonist. In this fanfiction, he might be jealous of Naruto's new god - like gaming powers and try to steal them for his own experiments.
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.
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.
One possible plot could be that Naruto, under Kaguya's training, gains godlike powers at an accelerated rate. He might learn ancient and powerful jutsu that were once exclusive to Kaguya. This could lead to him facing new and extremely powerful enemies, perhaps even threats from other dimensions. With Kaguya's guidance, Naruto could also gain a deeper understanding of the chakra and its origins, and use this knowledge to reshape the ninja world for the better.
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.
One potential antagonist could be an ancient evil that is awakened by Ichigo's newfound power. This entity might see Ichigo as a threat or as a means to achieve its own dark goals.
If it's a crossover with the One Piece world, Blackbeard could be a potential bad guy. His ability to steal Devil Fruit powers and his ambition to become Pirate King could lead to a clash with Gohan. Gohan's pure - hearted nature would be in opposition to Blackbeard's more devious ways, and their battle could be epic, with Gohan's ki powers against Blackbeard's dark powers.
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 the remaining Otsutsuki clan members. Since Naruto has merged with Kaguya, they might see this as a threat to their plans for the ninja world or a perversion of their bloodline. They could try to either eliminate the merged Naruto - Kaguya or control it for their own purposes.