Well, it could be that Snape has always had a soft spot for Harry, more than he lets on. And when he starts to suspect Dumbledore's motives regarding Harry, he decides to take action. For example, if Dumbledore is planning to sacrifice Harry in a way that Snape deems unjust, Snape, with his complex character and his own moral code, might choose to side with Harry. Fanfiction writers love to explore these deep and unspoken aspects of the characters.
In some fanfictions, Snape could have his own personal vendetta against Dumbledore. Maybe Dumbledore has wronged Snape in the past, and when he sees Harry as a potential victim of Dumbledore's schemes, he decides to help Harry. Another reason could be that Snape has a new understanding of the prophecy and believes that Dumbledore's way of handling it is wrong, so he steps in to help Harry.
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.
In a fanfiction, Dumbledore might steal out of desperation. Suppose there was a situation where a curse was about to be unleashed on Hogwarts, and the only way to stop it was by stealing a particular ingredient for an antidote from a place where it was not supposed to be taken. Dumbledore, seeing no other option, decides to steal it. His motive here is to save the school and its students, even if it means breaking the rules.
There are indeed. Fanfiction often takes the existing characters and relationships and turns them on their heads. In this case, Snape helping Harry against Dumbledore could be a result of Snape's long - held grudges against Dumbledore's actions or decisions. It's a creative way to explore the gray areas of these beloved characters.
Perhaps in the fanfiction, Snape falls in love with someone who has a vendetta against Dumbledore. This new love interest could convince Snape that Dumbledore is not as noble as he seems. Love can be a powerful motivator, and if Snape is truly smitten, he might be swayed to turn against his former ally.
One possible motive could be that Snape is still deeply influenced by his loyalty to Voldemort in this fanfiction. Maybe Voldemort has some hold over him that forces him to do the unthinkable. Another reason could be a misunderstanding. Snape might believe that Harry has turned to the dark side or is about to, and he decides to take preemptive action to stop what he thinks will be a great evil.
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.
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.
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.
Perhaps Harry has been misled by someone he trusts. They could have filled his head with lies about Dumbledore, making Harry think that Dumbledore is actually a threat. And his motive would then be to protect the wizarding world from what he believes is a hidden danger in Dumbledore.
Perhaps in this fanfiction, Dumbledore has a secret plan related to Harry's power. He might think that by kidnapping Harry, he can train him in isolation to fully develop his magical abilities without the distractions and potential dangers at Hogwarts. It could also be that Dumbledore is trying to hide Harry from Voldemort in a way that no one would suspect, as Voldemort would never think Dumbledore would use such extreme measures against Harry.