Maybe the main antagonist is actually a group of people within Konoha. They might be some of the elders who think Naruto's isolation is a threat to the village's stability. So they send people after him to bring him back, which Naruto sees as an intrusion and they become the antagonists in his eyes.
In this fanfiction, it's possible that the Nine - Tails itself could be the main antagonist. Since Naruto wants to be left alone, the Nine - Tails, which is always there inside him, might start causing trouble. It could be trying to take over Naruto's body or influence his actions in a way that makes it even harder for Naruto to have the peace he desires.
It could be a new and powerful dark ninja who thrives on isolation and wants to keep Naruto alone. He might see Naruto's solitude as a weakness to be exploited.
There's a possibility that the main antagonist is an internal force within Naruto himself. His desire to be alone could be a manifestation of some dark part of his psyche. This 'inner antagonist' could be trying to make Naruto cut himself off from his loved ones completely, leading him down a path of self - destruction. And Naruto has to fight this internal battle while also dealing with any external threats that come his way during his isolation.
Well, it could be about Naruto being constantly pestered by someone, like a villager who doesn't trust him because of the Nine - Tails inside him. So he just wants to be left alone to train and prove himself. He might go off to some secluded place in the forest to practice his jutsu without any distractions.
It could be a new dark wizard who is more powerful and cunning than Voldemort. This wizard might have been in hiding all this time, biding his time to take over the wizarding world. With Harry being alone, he would pose a great threat as Harry doesn't have his friends to support him in this fight.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
A powerful dark wizard who has a vendetta against Natsu. Maybe he blames Natsu for something that happened in the past, like the destruction of his dark guild by Fairy Tail. So, when Natsu and Happy leave Fairy Tail, he sees it as an opportunity to get revenge.
Voldemort could still be the main antagonist. Even though Harry is alone, Voldemort would see him as a threat and continue to send his Death Eaters after him. Harry would have to face these attacks all by himself, which would make the story very intense.
It could be Tartarus itself personified. As Percy is alone in this terrifying place, Tartarus could take on a form and directly oppose him. It would use all the horrors and challenges of the place to try and break Percy.
A group of rogue ninja who are hunting nekoshou for their special powers could be the main antagonists. They see Naruto's newfound connection with the nekoshou as a threat and try to eliminate him and the nekoshou he is protecting.
It could be a bully in the village. This bully could constantly pick on Naruto because of his status as the Jinchuriki of the Nine - Tails. He might try to steal Naruto's food or prevent him from playing with other kids.