Perhaps the writer wants to explore the nature - vs - nurture concept. Harry grew up in a difficult environment, and in fanfiction, this could be twisted to make him turn to evil. Another reason might be to introduce a more complex villain. Instead of a typical bad guy, having Harry as a secretly evil character adds a new layer of depth to the story.
In a lot of these fanfictions, it could be that Harry has a secret mentor. This could be an old wizard who has been secretly guiding Harry in potions, away from the prying eyes of the Hogwarts staff. This mentor could have seen Harry's potential early on and decided to help him develop his skills in private. Another aspect could be that Harry's own determination and his need to prove himself in a different area other than Quidditch or fighting Voldemort drives him to secretly practice and become good at potions. Also, the idea that there are hidden aspects of magic within him, perhaps related to the founders of Hogwarts, that only manifest in his potions - making ability.
Power hunger could be a motive. Tony already has a lot of power with his technology, but if he becomes obsessed with having more and more, it could lead him to evil. He might start to see others as obstacles to his power gain.
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.
In some fanfiction, Harry might be portrayed as secretly evil. This could be due to a writer's desire to explore different character arcs. Maybe they want to show how power could corrupt him or how a hidden past could change his true nature.
Jealousy could be a big motive. Harry is often the center of attention, and Draco, who is used to being in the spotlight in his own Slytherin circle, might be jealous. So he punishes Harry to try and knock him down a peg or two.
One possible motive could be revenge. The Dursleys treated Harry awfully for years, so in fanfiction, he might reach a breaking point. Another could be self - defense if the Dursleys in the fanfiction were to take their abuse to an extreme level.
One possible plotline could be that they start to secretly help each other with their studies. For example, Draco might be struggling with a certain type of magic that Harry is good at, like Patronus Charms. In secret, Harry could give Draco some tips. Another could be that they team up to solve a mystery in Hogwarts that no one else is aware of. They might discover a hidden chamber or a secret spellbook together. They would have to keep their friendship a secret because of the rivalry between Gryffindor and Slytherin. Their friendship could also be tested when their respective houses are in competition, but they still find ways to support each other on the sly.
One possible motive could be misinformation. If Harry is fed false information about Sirius being a traitor or a danger, he might act on it. For instance, if a well - disguised Death Eater manages to convince Harry that Sirius has joined Voldemort, Harry, in his haste to protect others, could attack Sirius.
Well, in this sort of fanfiction, Ginny's motive could be a complex web of emotions. She might be under the influence of a dark spell. Or perhaps she has been misinformed about Harry's role and believes that by giving him to Voldemort, she's actually saving the wizarding world. It could also be a case of extreme jealousy, if the writer wants to explore a really twisted version of her character.
Jealousy might be a motive. If Hermione is constantly outshining them in academics or getting more praise from teachers, they could become envious and turn against her.