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 has risen to power. Maybe someone who was in the shadows during Voldemort's time and now sees an opportunity with Harry being alone. This new antagonist could have unique and dangerous magic abilities.
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.
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 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.
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.
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 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.
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.
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 power - hungry merman who wants to rule over all the mer - people. He sees Harry as a threat because Harry has some special powers or a claim to the throne that he doesn't want to share.