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.
Maybe an ancient evil ninja who was sealed away long ago but has now been released. This antagonist could have powers that nullify any communication or summoning jutsu, forcing Naruto to fight alone. He would be extremely powerful and know many forgotten and deadly jutsu.
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 someone from the village who doesn't understand Naruto's need for solitude. Maybe a council member who thinks Naruto is shirking his duties and tries to force him back into the spotlight.
Voldemort could still be a great antagonist even in a story where Harry battles alone. His power and the threat he poses are well - established in the Harry Potter universe.
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.
The main antagonist could be an internal one - Harry's own guilt. It's like a dark shadow that follows him everywhere. He wants to be alone to escape from it, but it keeps haunting him. It makes him question his every move and decision, and it's this internal struggle that could be seen as the main 'antagonist' in the fanfiction as it constantly opposes his desire for peace and solitude.
A group of bandits might be the main antagonists. They see Percy as someone they can easily rob or enslave since he is all alone. Percy would then have to use his skills to outwit them.
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.