It could also be that Harry has a different vision for how to deal with the main threat in the wizarding world. Dumbledore's plans might seem too slow - paced or too conservative to Harry. He may believe that his own more direct and bold approach would be more effective, and thus decides to destroy Dumbledore's plans to implement his own.
One possible motive could be that Harry discovers some long - hidden secrets about Dumbledore that he feels are unethical or immoral. For example, if he finds out that Dumbledore had some ulterior motives in his actions towards Harry throughout the years. Maybe Dumbledore was using Harry for a greater plan that involved a lot of sacrifice on Harry's part without his full knowledge or consent.
One possible motive could be to explore a dark and alternate universe. The writer might want to see how the 'Harry Potter' world would change if such a drastic event occurred. Another reason could be to analyze the characters from a different perspective. By making Harry the destroyer of Dumbledore, it forces readers to re - evaluate both characters.
Well, perhaps Harry is under the influence of a dark spell that makes him lose control and lash out at Dumbledore's office. Maybe he discovers something in the office that he believes is a great betrayal by Dumbledore and in his rage, he starts to destroy things.
Well, in some fanfictions, Harry might attack Dumbledore if he discovers that Dumbledore has been using him as a pawn in a bigger game all along. This feeling of betrayal could drive him to lash out. Also, if there is a prophecy that he misinterprets to mean Dumbledore is a threat to his future or the future of his friends, that could be a motive.
One possible plot could be that Harry discovers some hidden motives behind Dumbledore's actions. Maybe he finds out that Dumbledore was using him in a way he didn't expect, like in a grand scheme against Voldemort that put Harry in more danger than necessary. So, Harry decides to expose these plans to the wizarding world, which would cause a huge upheaval in the relationships between characters.
One possible motive could be that Dumbledore saw a future where Harry's parents' deaths were necessary for a greater good. Maybe he knew that Harry would be the only one to defeat Voldemort in the end, and their deaths were a catalyst to set Harry on that path.
It could be that Dumbledore is afraid of what Harry might do if left to his own devices. Harry has a lot of power, and Dumbledore may worry that he could be swayed by the wrong people or ideas. So, in an attempt to keep Harry on the 'right path', he resorts to trying to control him. But this also shows a lack of faith in Harry's character and judgment.
Some writers might do it to create a sense of shock. They want to break the traditional view of the Dumbledore - Harry relationship and get readers' attention. It's a way to be different in the vast sea of fanfiction.
Maybe Dumbledore believes that Harry has some hidden power that is being corrupted by the environment at Hogwarts. So, he kidnaps Harry to a secluded place to train him and help him control this power without any distractions or negative influences from other students or even some of the teachers.
Maybe Harry uncovers evidence that Dumbledore had been manipulating him all along. Like Dumbledore knew more about Voldemort's connection to Harry than he let on, and he was using Harry as a pawn in a bigger game. Harry, feeling betrayed, decides to expose Dumbledore's true nature, which would shatter the positive image everyone had of him.