Another option for the main antagonist could be a group of ninjas who are against any form of deviation from the traditional ninja ways. They see Naruto's goth transformation as a corruption of the ninja code. They would be constantly trying to hunt him down and make him conform to the old ways, creating a lot of conflict for Naruto throughout the fanfic.
Maybe a new character could be introduced as the main antagonist. A powerful goth - like ninja from a far - off land who is jealous of Naruto's newfound dark power. This character could have a similar set of skills as Naruto but with a more malevolent intention. He might try to steal Naruto's power or defeat him to prove his own superiority in the goth ninja world.
It could be the village elders. In the original series, they often made decisions behind the scenes. In a 'naruto goes rogue' scenario, they might be the ones who push Naruto to the edge. For instance, they could be plotting against him to maintain their power in the village.
Maybe Danzo could be the main antagonist. He has always been a bit of a shady character in the Naruto series. He could see Naruto as a threat and use his influence to frame him and send him to prison to further his own political or power - hungry goals.
It could be Voldemort if the story takes place during the time he was a threat. Naruto's arrival might disrupt his plans in some way, so he would see Naruto as an obstacle.
Well, in a 'naruto goes goth fanfic', perhaps Naruto has an encounter with a powerful and dark entity. This entity influences him to embrace the goth aesthetic. He could start using different jutsu that have a darker, more menacing look. His friends might be initially shocked but then try to understand what led him to this change. He might even change the look of his home to be more gothic, with dark curtains and spooky decorations.
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 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.
A group of Death Eater sympathizers within the Ministry could be the main antagonists. They still hold onto the old pure - blood supremacist ideals and see Hermione, a Muggle - born witch, as a threat. So they fabricate evidence against her and send her to Azkaban to send a message to all Muggle - borns that they are not welcome in the new wizarding order they are trying to create.
It could be a dark wizard who has infiltrated Hogwarts under a disguise. Percy might be the one to first suspect this wizard's true identity.