In some fanfictions, the Order might kidnap Hermione because they believe she has some sort of dangerous knowledge that could fall into the wrong hands. They think that by taking her into their custody, they can protect that knowledge and keep her safe from the real enemies who might want to use her.
It could be a rogue member who has different ideas from the rest of the Order. Maybe someone who believes Hermione has some kind of power or knowledge that they want to use for their own purposes. For example, a character who is desperate for a solution to a dark magic problem and thinks Hermione can provide it.
Another reason could be to protect her from a prophecy. In the world of fanfiction, there could be a prophecy that foretells Renesmee's doom if she stays with the Cullens. So Jacob, thinking he's doing the right thing, kidnaps her to keep her away from that fate.
Another reason could be that Tsunade is trying to use Naruto for some sort of political leverage within the village or against other villages. She may think that having Naruto in her control gives her an advantage, but as the story unfolds, she realizes the error of her ways.
Sasuke might kidnap Naruto because he wants to prove his superiority. By taking Naruto captive, he can show that he is stronger and more in control. It could be a power play, where Sasuke is trying to assert his dominance over Naruto once and for all.
In some fanfictions, Vegeta could be under the influence of some external force. Maybe an evil entity has convinced Vegeta that kidnapping Goku is the key to achieving ultimate power. Vegeta, being power - hungry as he is, falls for it and kidnaps Goku. But later, he realizes his mistake and has to make amends, which can lead to an interesting story arc of redemption and friendship building between the two Saiyans.
Vlad could kidnap Danny in fanfiction for revenge. Maybe he blames Danny for something, like ruining his plans in the past. Or perhaps he wants to use Danny as a bargaining chip against the other ghosts. He might think that by having Danny under his control, he can gain more influence in the ghost world.
He could kidnap her because he believes she's in immediate danger. Natsu is very impulsive and might not have time to explain things properly, so he just takes her away to keep her safe.
At first, Hermione would be shocked. But then, she would quickly compose herself. She could play along with Draco and Blaise for a while, pretending to be compliant while she actually gathers information about their motives and the place where they are holding her. She might also try to turn them against each other by highlighting their differences in goals or personalities. Given her intelligence, she would surely come up with a clever plan to get out of the situation.
One possibility is that the Sith or some dark side cult would kidnap Luke. They'd want to either corrupt him or stop him from being a threat to their plans. Luke is a powerful Jedi, and getting him out of the picture would be a major advantage for the dark side.
For Hermione, her character would be fighting against this unjust situation. She would be using her wits to try and escape. Meanwhile, Draco and Zabini may start to have second thoughts as they see Hermione's strength and determination. Maybe Draco's motivation changes from self - interest to a more complex mix of respect and fear for Hermione.