The main antagonist could be a dark entity that somehow influenced the events leading to Naruto's imprisonment. It wants to plunge the world into chaos and sees Naruto's godlike power as the only thing that can stop it. So, it tries to get rid of Naruto by causing more trouble in the village, making the villagers turn against Naruto again so that it can continue with its evil plans.
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.
Maybe it's a group of corrupt elders within Konoha itself. They were the ones who put Naruto in jail in the first place to maintain their hold on power. Now that he's back and more powerful, they try to undermine him at every turn, fearing that he'll expose their misdeeds and take away their power. They could be the main antagonists as they try to stop Naruto from bringing positive change to the village.