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.
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.
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.
Well, perhaps in this fanfiction, Harry has had enough of the constant battles and drama. He just wants a break from his friends too, not because he doesn't love them, but he needs time for himself. He could find an abandoned cottage and start a simple life there, growing his own magical plants and spending his days reading ancient magic texts that he never had time for before. He's basically trying to find peace away from all the chaos.
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.
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 Voldemort. If this story is set during the time when Voldemort was still a threat, he might be trying to stop Harry from getting home. Maybe he has a plan that involves keeping Harry away from the safety of his home so that he can be more easily attacked or manipulated.
Another possibility is that the antagonist is a powerful and ancient magical being that has its own agenda. This being doesn't want Harry to reach his full potential as Dumbledore hopes because it fears that a powerful Harry could disrupt the balance it has been maintaining in the magical world for centuries. So it tries to create obstacles for Dumbledore's efforts to help Harry.
Maybe Naruto has had enough of the chaos in the ninja world. He could be tired of all the battles and political intrigue. So, he decides to find a secluded place, perhaps a small island, where he can live in peace and train by himself without any distractions.
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.