Perhaps it's an old enemy from Harry's past, like Draco Malfoy who has turned to the dark side completely. He blames Harry for all his misfortunes and decides to cage him without his glasses as a form of cruel punishment.
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.
Voldemort or his Death Eaters are likely antagonists. They have always been out to get Harry, and chaining him up without his glasses would be a cruel and effective way to subdue him.
Well, perhaps in this fanfiction, Harry could be imprisoned by some dark wizards. Without his glasses, he'd be at a great disadvantage, relying more on his other senses and magical instincts. Maybe he uses his Parseltongue ability to communicate with a snake in the cell to help him escape.
One possible plot could be that Harry is captured by some dark wizards who know his power lies in his eyes (with his glasses being a symbol of his clear - sightedness in magic). They cage him up to weaken him, perhaps trying to prevent him from seeing certain magical signs or spells. Without his glasses, he's disoriented at first but then uses his other senses and inner magic strength to start fighting back.
Obviously, Harry Potter himself would be at the center of it. His friends Ron and Hermione would likely be involved too. They might be trying to protect Harry or stop him from getting into more trouble. Also, Draco Malfoy could be involved. He might take advantage of Harry's lack of glasses and start a fight, thinking he can easily defeat Harry when he's not seeing clearly.
Harry could be at a significant disadvantage without his glasses. He might misjudge distances when Nagini attacks, making it more dangerous for him. However, this could also lead to the discovery of new magical abilities, like a form of magic - based echolocation. Nagini might be used by the dark forces to take advantage of Harry's impaired vision.
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.
Perhaps a magical creature that has made the island its territory. This creature doesn't want outsiders like Harry and his friends interfering. It sees Harry's glasses as a strange and foreign object and will do anything to keep them from leaving the island. It could be a giant spider - like creature that spins webs to trap intruders, just like the acromantulas in the Harry Potter series.
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.