Maybe Rowle is under the orders of a more powerful dark wizard. In the world of Harry Potter, there are always those higher - ups in the dark side who might want Hermione for her knowledge of magic, especially things like ancient spells and magic theory. So Rowle could be tasked with kidnapping her for that purpose.
Another motive could be related to her family. Maybe there was some sort of blood feud or an old grudge against the Grangers. The kidnappers could have thought that by taking Hermione, they could get revenge on her family. In some fanfictions, there are secret magical families that have long - standing rivalries, and Hermione's kidnapping could be part of that.
One possible motive could be to use Sakura as bait. Maybe Sasuke is trying to lure Naruto to a certain location. He knows Naruto cares deeply about Sakura, so he figures Naruto will come after her.
It could also be a result of some external influence, like a dark magic spell that has clouded Ron's judgment. This spell could be making him act against his normal character and do something as extreme as kidnapping Hermione. However, in the end, he would likely break free from this influence and realize the error of his ways.
One possible motive could be revenge. Maybe Draco feels that Ginny or the Weasleys have wronged him or his family in some way. For example, if he blames Ginny for getting Harry Potter on their side all the time which has made things difficult for the Malfoys at Hogwarts. Another motive could be related to power. He might think that by kidnapping Ginny, he can gain some sort of leverage over the Order of the Phoenix or Dumbledore's side. It could also be out of jealousy. If he has some unspoken feelings for Ginny but she's always with Harry, he might kidnap her in a fit of jealous rage.
One possible motive could be that Bakura wants to use Anzu as a bargaining chip. Maybe he's trying to get something from the main characters, like a powerful item or information. Another motive might be related to some sort of revenge. He could think that Anzu is close to someone he has a grudge against, so by kidnapping her, he can cause pain to that person.
One possible motive could be to use Naruto as a bargaining chip. Itachi was a complex character with his own goals related to the safety of the Hidden Leaf Village in some ways. He might have thought that by kidnapping Naruto, he could influence the village's decisions. For example, he could try to stop certain actions the village was planning that he believed would lead to more harm. Another motive could be related to the Nine - Tails within Naruto. Itachi might have wanted to study or control the power of the Nine - Tails for his own purposes, perhaps thinking it could be a way to protect Sasuke in a different manner.
Perhaps it's about love in a twisted way. Sebastian might be obsessed with Clary and think that by kidnapping her, he can make her his. In some fanfictions, characters with a warped sense of love do extreme things like this. He could also be trying to use Clary as a pawn in a larger scheme against the Shadowhunters. By having her in his control, he can manipulate the situation to his advantage.
One possible motive could be misinformation. Maybe Bucky was misled to believe the OC was a threat to someone he cares about. So, he kidnapped the OC to prevent them from causing harm.
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 it's because the fanfiction showcases Hermione's intelligence in new and exciting ways. In the original stories, Hermione is already very smart, but the fanfiction might take it to another level, like having her solve even more complex magical problems.