It could be the wizarding society itself. If Harry gives up his humanity, the wizarding society might turn against him. They could become the antagonists as they try to stop Harry from causing more harm. The Ministry of Magic could lead the charge, fearing that Harry's new state will disrupt the peace and order they have been trying to maintain. They might use all means necessary, including dark magic if they have to, to subdue Harry.
One possible plot could be that in the fanfiction, Harry Potter is faced with an extremely difficult situation. Maybe he has to make a deal with a dark force to save his friends. For example, the dark force offers to spare his friends' lives if he gives up his humanity. This would lead to him losing his ability to feel emotions like love, compassion, and kindness. He might then start to act in ways that are completely out of character, using dark magic without hesitation and causing chaos in the wizarding world.
It could be the Death Eaters. They might see Harry as a big threat, and by caging him up without his glasses, they aim to make him vulnerable. They know his glasses are an important part of his identity and his ability to see clearly in the magical world, so they take that advantage away from him.
Perhaps there's a member of the royal court who is secretly envious of Harry's power and tries to undermine him. This person could be plotting against Harry and trying to make the queen believe that he is a danger rather than an asset. They might spread false rumors or create false evidence to get rid of Harry.
It could be a new dark wizard who is jealous of Harry's ability to lift Excalibur. This wizard might want the sword for himself to gain ultimate power. He could start causing chaos in the wizarding world, trying to draw Harry out and take the sword from him. He might even team up with some of the Death Eaters who are also interested in the power the sword could bring.
Maybe the main antagonist is a dark force that has been slowly taking over the alliances from within. Harry notices this and decides to cancel the alliances to prevent the dark force from spreading further. This dark force could be something like an ancient evil that has awakened and is using the alliances as a way to gain a foothold in the wizarding world.
A new and mysterious dark ninja could be the main antagonist. This character might have a special ability to corrupt others. They target Naruto specifically because of his power and influence. By using some form of dark jutsu or psychological manipulation, they make Naruto lose his humanity, turning him into a weapon against the very people he used to protect.
It could be a new player on the team who is jealous of Harry's skills and popularity. This new player might spread lies about Harry, turning the other team members against him. So the new player would be the main antagonist in this scenario.
It could be a new dark wizard who has been secretly searching for the Death Stone. Maybe someone who was in the shadows during Voldemort's time and now sees an opportunity to rise with the power of this stone.
It could be Draco Malfoy. He might be jealous of Harry getting certain important mail, like letters from Dumbledore or invitations to exclusive wizarding events. So, he uses some underhanded means to make Harry's mail disappear. Draco would think it's a funny prank at first, but when Harry starts to fight back, it turns into a more serious conflict between them.
It could be a new dark wizard we haven't seen in the original series. Maybe someone who has a vendetta against Hogwarts and manipulates Harry into doing the dirty work of destruction.