Maybe one of the rogue ninja who has a vendetta against Naruto's village. They could plant evidence to make it look like Naruto is working with them or has committed a crime against another village. Their goal would be to not only get Naruto out of the picture but also to cause chaos in his village. So, this rogue ninja would be the main antagonist as they work to keep Naruto in jail.
It could be Danzo. He's always been a bit of a shady character in the Naruto series. He might see Naruto as a threat to his power and influence in the village. So, he could frame Naruto for some crime and get him sent to jail just to eliminate his competition.
The Joker could be the main antagonist. Even though Batman is in jail, the Joker could find a way to continue his chaos - making. He might try to get into the prison to torment Batman or use the situation to his advantage by causing mayhem in Gotham City without Batman there to stop him.
The main antagonist could be a new character, a corrupt official in the Ministry of Magic who wants to get rid of Harry because he's seen as a threat to their power. This person could manipulate the legal system to send Harry to jail.
The Kingpin could be a likely antagonist. He has the resources and the motive to frame Spider Man and get him out of the way. He could use his criminal connections to plant false evidence and make sure Spider Man ends up in jail.
It could be a new character, perhaps a corrupt wizard in the Ministry of Magic who has a vendetta against the Dursleys for some reason. This wizard might make their time in jail even more difficult by withholding basic rights or subjecting them to unfair treatment. And he might be doing all this for his own gain, like trying to steal the Dursleys' Muggle money or something.
It could be the same people who framed Naruto and got him jailed in the first place. Maybe a group of rogue ninjas or corrupt village leaders who see Naruto as a threat to their power.
Maybe it could be a new character who is a combination of ninja and wizardry evils. This character could be jealous of Naruto's unique abilities that bridge the gap between two different worlds and wants to stop Naruto from uniting the ninja and wizarding communities against him. They could have powers that are a mix of dark magic and some dark ninja jutsus.
The main antagonist could be Naruto himself in a sense. Since he has gone insane, his actions are now unpredictable and harmful to the people around him. His former friends, like Sakura or Kakashi, might have to step up and try to stop him, seeing him as the new threat.
The Hidden Leaf Village itself could be the main antagonist. If they turn on Naruto for no good reason, they become the force he has to fight against as a rogue ninja.
It could be a powerful ninja from another village who saw Naruto as a threat even when he was in jail. This ninja might have been plotting to take over Konoha while Naruto was out of the picture. Now that Naruto is out and godlike, they see him as an even bigger obstacle to their plans.
Another possibility is that there is a rogue ninja in Kumo who uses Naruto's neglected state to his advantage. He might try to manipulate Naruto into doing things that would be bad for both Naruto and Kumo, all while remaining in the shadows and making it seem like Naruto is acting on his own accord.