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.
Another possibility is that an old enemy, who has been biding their time, sees Naruto's release as an opportunity to finally defeat him. This could be someone like Orochimaru, who might have some new and more dangerous experiments and wants to use Naruto for them now that he's out of jail.
There might be a new villain who emerges after Naruto's release. This villain could be someone who was using Naruto's imprisonment as a distraction to carry out their own evil plans, like stealing powerful ninja artifacts or trying to take over the ninja world while everyone was focused on Naruto.
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.
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.
In this 'Naruto released from jail' fanfiction, it could be that Naruto was jailed because of some false accusations related to a powerful and dangerous jutsu he was suspected of misusing. After his release, he embarks on a journey to find the real source of the jutsu and prove that it can be used for good. Along the way, he meets new allies and old enemies, and has to use his wits and strength to overcome various obstacles.
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.
Madara Uchiha could also be a main antagonist in this fanfiction. He has grand plans for the ninja world and the released Kyuubi could be a key part of his scheme. Since Naruto is dead and can't oppose him, he might try to use the Kyuubi to reshape the world according to his vision. He has the power and the ambition to be a major threat in this situation.
One possibility could be that Naruto emerges from jail with newfound powers. He might have been framed and while in jail, he discovers a hidden power within himself. He then uses this power to clear his name and also to protect the village from a new threat that emerged while he was incarcerated.
Perhaps the main antagonist is a corrupt official within the Hidden Leaf Village itself. This person was the one who arranged for Naruto's imprisonment in the first place and now that Naruto is out, they will do everything to stop him from uncovering their misdeeds. They might even team up with external enemies to achieve their goals.
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.