One possibility is that Dumbledore has discovered some hidden power within Harry that he fears Voldemort might try to corrupt. So, by kidnapping Harry, he aims to train him in isolation to master this power without the influence of others. However, this would be a very controversial move as it goes against the trust that Harry has placed in Dumbledore throughout the series.
In this kind of fanfiction, it could be that Dumbledore has some very complex motives for 'kidnapping' Harry. Maybe he wants to protect Harry from a danger that he can't explain openly. For example, there might be a powerful dark wizard who has found a way to spy on Hogwarts and Dumbledore believes that keeping Harry in a secret location is the only way to keep him safe.
Perhaps Dumbledore has been misled by some false prophecy or information. He might think that Harry is in immediate danger of turning to the dark side. So, in his over - protective way, he kidnaps Harry. But this would lead to a huge rift between Harry and his friends at Hogwarts, who would be very confused and likely try to rescue him.
In this fanfiction scenario, Snape might be under the influence of a dark spell or some form of blackmail. He kidnaps Harry as a result. However, Harry, being the resourceful character he is, might start to figure out Snape's true situation and try to help him break free from whatever is controlling him.
Another aspect could be that Dumbledore is being controlled or influenced by some external force. In the fanfiction, this could lead to a very interesting story where Harry has to figure out how to break Dumbledore free from this control while also escaping from his 'kidnapper'. It would be a total role - reversal from the original story.
A plot twist could be that Dumbledore faked his own death to test Harry's loyalty. But when Harry starts to turn on him, Dumbledore realizes his plan backfired. This would create a lot of tension and conflict between them, and also force Harry to re - evaluate his entire relationship with Dumbledore.
Well, perhaps Dumbledore has some dark secret and believes Harry is the key to it. He might kidnap Harry to keep him away from Voldemort in a very unorthodox way. Maybe he wants to train Harry in isolation for some super - powerful magic that he doesn't want Voldemort to find out about.
Maybe the 'evil' Dumbledore was a future version of himself who had been corrupted by time - travel gone wrong. Harry, not fully understanding the situation, battles and defeats this future Dumbledore. This could then lead to a complex time - paradox plot where Harry has to find a way to fix the timeline and save the real Dumbledore from this fate.
One common plot twist is that Dumbledore knew all along about Harry being his grandson but kept it a secret to protect him. Another could be that there's a dark family secret that comes to light, like a curse on the family line that Harry has to break.
It could also be that there is a mole in the Order. Harry suspects someone close to him in the Order is actually working for Voldemort. Feeling unsafe and not knowing who to trust, he chooses to escape to protect himself and those he cares about. He then embarks on a solo journey to expose the traitor and fight Voldemort on his own terms.
A really interesting plot twist might be that Voldemort is being controlled by an even darker force, and Harry has to figure out a way to break that control while being held captive. Or perhaps Harry's friends, thinking he is dead, accidentally start a chain of events that end up helping Harry escape in a very unexpected way. For example, Hermione might cast a spell that was supposed to be for protection but ends up creating a portal right in Voldemort's lair.
One possible plot twist could be that without his glasses, Harry has a hard time recognizing his captors. It might turn out that they are people he thought he could trust, like some seemingly friendly Hufflepuffs who are actually under the Imperius Curse. This would add an element of betrayal and confusion to the story.
A plot twist could be that Harry's kidnapping and loss of glasses is the result of a time - travel mishap. A future version of himself (or someone else) accidentally causes the present - day Harry to be kidnapped and lose his glasses. The future version is trying to change the course of events for the better but ends up creating chaos in the present. Harry, without his glasses, has to figure out what's going on and how to fix the time - line while also escaping from his kidnapper. Another twist could be that the kidnapper is actually an undercover Auror gone rogue who is using Harry as a bait to draw out a much larger and more dangerous criminal organization. Harry's glasses are lost in the process, and he has to figure out who to trust among his captors.