There could be a mysterious organization that is secretly manipulating events in the ninja world. They see Naruto as a threat to their plans because of his influence and power. As a young Jonin, Naruto uncovers their existence and has to fight against their schemes, which are far - reaching and complex.
It could be a new group of rogue ninja. They might be after some powerful jutsu or artifact in the Hidden Leaf. Naruto, as a young Jonin, would be one of the main defenders against them. They could have unique abilities that Naruto and his team have never faced before, making the battles intense.
One possible plot could be Naruto facing new and tougher challenges as a young Jonin. He might be assigned to lead a special mission that requires him to use his unique skills and leadership abilities. For example, he could be sent to a border area where there are constant skirmishes with enemy ninja. Naruto would have to strategize and protect his team members, all while dealing with the expectations that come with being a Jonin.
The Akatsuki could still be a major antagonist. Even if Naruto is emperor, they might oppose his rule as it goes against their own goals of chaos and obtaining the tailed beasts.
One possible antagonist could be a jealous noble from Naruto's own kingdom who feels that Naruto doesn't deserve the prince title. This person might try to undermine Naruto at every turn, spreading false rumors about him or trying to sabotage his diplomatic efforts.
Another possible antagonist could be a fellow inmate who has a personal vendetta against Naruto. Maybe this inmate was once on the wrong side of Naruto's actions outside the prison and now sees this as an opportunity for revenge. He could try to undermine Naruto at every turn, from spreading false rumors about him to physically attacking him when the guards aren't looking.
Another option could be Orochimaru. He has his own motives and is always looking for power. He could be the head of a powerful gang in the criminal underworld of the Naruto world. He would constantly be trying to capture Naruto or his friends to use them for his experiments or to gain more power over the ninja world.
The Akatsuki could still be the main antagonists. They might be interested in Naruto's tails for their own dark purposes, like using their power to create a super - weapon or gain control over the ninja world. Another option could be a secret group of rogue ninjas who have a vendetta against the Uzumaki clan and see Naruto's tails as a symbol of their power that they want to destroy.
One potential antagonist could be a new and mysterious organization that is similar to Akatsuki but with different motives. They might be interested in using Daisuke to open a portal to a different dimension or something like that. They would be constantly trying to kidnap Daisuke and force him to cooperate. Also, Orochimaru or his remaining followers could be antagonists. Even though Orochimaru has changed somewhat in the series, there could still be some of his followers who are more radical and want to use Daisuke for their dark experiments, believing that he has some special chakra or ability that could help them achieve their twisted goals.
There could be a new, mysterious force that is neither from the Naruto world nor fully part of the Olympian world. This force wants to disrupt the balance between the two worlds and sees Naruto as the key to achieving its goals. It could manipulate both sides and create chaos.
The ANBU black ops could also play the role of antagonists. They are the ones who carry out the village's more secretive and sometimes morally gray missions. If they are ordered to hunt Naruto down unjustly, they would be in Naruto's way and could be the reason for his violent reaction towards Konoha.
Well, perhaps there could be a powerful underwater clan that sees Naruto as an abomination because he is a half - human, half - Neptune's son. They view his existence as a threat to the balance of the ocean realm and the ninja world. They send their best warriors to stop Naruto from growing in power and spreading his influence. Also, a mad scientist - type character who wants to experiment on Naruto to unlock the secrets of his Neptune - heritage could be an antagonist.