There could be a group of anti - military rebels outside the military. They see the military as a tool of oppression and are constantly causing trouble. Percy might have to deal with them, either through combat or trying to negotiate and understand their point of view.
Maybe some of the more malevolent Primordials themselves could turn out to be antagonists. If Percy refuses to do their bidding or stands in the way of their plans, they would oppose him. Also, there could be ancient creatures that are awakened by Percy's presence among the Primordials and they see him as an intruder to be eliminated.
It could be a group of rogue entities that are not fully part of the new pantheon but exist on its fringes. They might oppose Percy's presence because they fear he will disrupt the balance that they are trying to manipulate for their own gain.
Some of the more corrupt and power - hungry members within the mafia that Percy joins could be antagonists. They might not like Percy's attempts to change things or might be jealous of the skills he brings. For example, an old - school mafia capo who doesn't trust this new kid with all his strange abilities.
It could be the navy. They see pirates as outlaws and would be determined to capture Percy and his crew. They might have better - equipped ships and more trained soldiers, making them a formidable foe for Percy and his fellow pirates.
Monsters could also be antagonists. With Percy in a new, more powerful state as a godling, there could be new and more powerful monsters that are drawn to his power. These monsters might be stronger and more intelligent than the ones he faced as a demigod, and they could be after his godly essence or trying to use him for their own dark purposes.
A powerful sorcerer who wants to use Percy for his own dark purposes could be an antagonist. This sorcerer might see Percy's unique abilities as a key to unlocking some sort of forbidden magic.
It could be the ninja from Naruto's former village who don't want him to succeed in his new place. They might see his new - found influence as a threat and try to undermine him.
It could be Orochimaru. He's always been interested in power and the hunt for powerful things. He might see fem Naruto as a threat or a potential source of power. He could try to capture her or stop her from achieving her goals in the hunt.
The main antagonists could be some of the conservative Iwa ninjas who oppose Naruto joining their village. They might see him as a threat to their traditional ways and values. Also, there could be some rogue ninjas from other villages who target Naruto because they see him as an easy target now that he's in a new and unfamiliar environment.
One potential antagonist could be an ancient magical entity that has been awakened by the experiments of the Unspeakables. It sees Harry and the Unspeakables as a threat to its existence and tries to destroy them. Additionally, there could be a group of anti - Ministry wizards who believe that the Unspeakables are dabbling in dangerous magic and they target Harry as a symbol of the Unspeakables' activities.