It could be part of a magical curse. The curse made him lose his glasses and trapped him in a cage. Maybe it was cast by a jealous student at Hogwarts who wanted to get back at Harry for always being in the spotlight. In the cage, Harry has to figure out how to break the curse and get his glasses back, all while dealing with the limitations of his impaired vision.
Perhaps in this fanfiction, Harry is in a cage as part of a magical experiment. Some rogue wizards are trying to study how a wizard's magic is affected without their usual aids, like Harry's glasses. In the cage, Harry discovers new aspects of his magic that he didn't know before. He could start to manipulate the magical energy around him in different ways, even without clear vision, and eventually break free from the cage and confront those who put him there.
It could be a situation where Harry has been wrongly accused. Some overzealous magical law enforcers chain him up and confiscate his glasses as a form of punishment before a proper trial. This would create a lot of internal conflict within Harry, feeling betrayed by the very system he has been fighting for.
Another reason might be related to a new magical artifact or potion. Harry might have come across something that had an unforeseen effect on his glasses. It could be that a new charmed item he was using interacted with his glasses and caused them to disappear.
One possible plotline could be that Harry is captured by some dark wizards who want to interrogate him about the Order of the Phoenix. Without his glasses, he's at a disadvantage, trying to sense his surroundings magically while tied up. They might be trying to find out the location of the Order's secret hideout.
One possible scenario could be that he's being dragged by some dark magic force in a forbidden part of Hogwarts. Maybe he lost his glasses during a fight or while being chased, and now he's in a vulnerable state. Without his glasses, his vision is blurry, adding to the sense of danger and confusion.
Hermione could be one of his allies. She's smart and resourceful, and she would do everything she can to get Harry out of the cell. Even without his glasses, Harry would recognize her voice and know he can trust her. Another possible ally could be Dobby. Dobby has a special connection with Harry and his magic could be useful in getting Harry out of the cell, like apparating in to bring Harry his glasses or help him escape directly.
In fanfiction, if Harry Potter were without glasses, it would likely have a significant impact on his character arc. His glasses are not just a visual accessory but also a symbol of his 'nerdy' or 'outsider' status at the start. Without them, he could be more integrated into the 'cool' crowd at Hogwarts. He might also be more daring in his adventures as he wouldn't have to worry about his glasses getting broken or lost during battles or dangerous situations. This could lead to a more confident and perhaps even a more flamboyant Harry Potter in the fan - created stories.
One possible reason could be as a form of humiliation. His enemies might take his glasses to make him feel vulnerable and less in control. Without his glasses, Harry is severely visually impaired, so it's a way to undermine his confidence.
Another idea is that some Death Eaters find Harry without his glasses in a vulnerable state. They start by taunting him about his weakness without the glasses. Then they use dark magic to make him experience extreme pain, like a searing pain in his eyes as if they are trying to make him feel the 'punishment' for relying so much on his glasses. They might also try to force him to perform difficult magic tasks without being able to see clearly, and punish him severely when he fails.
One possible consequence is that he might get injured more easily. Without his glasses, his vision is impaired, and being blindfolded makes it even worse. He could trip over things, bump into walls or other objects, and get bruises or cuts.