Well, it could be a group of wizards who were influenced by a false prophecy. They believed that Hermione would grow up to be a great evil, so they kidnapped her at birth to try and stop her from fulfilling that so - called destiny. Another option is a powerful magical artifact that had some sort of sentience and saw Hermione as a threat. It used its powers to have her kidnapped. And then there's the possibility of a group of rogue Aurors who had gone bad. They might have thought they could use Hermione for their own illegal activities, like blackmailing the wizarding government by having control over a powerful future witch.
The potential kidnappers could be a secret society within the wizarding world that has its own agenda. They might believe that Hermione has a special power or connection that could either help or harm their cause, so they took her at birth to control that. It could also be a non - human magical being, like a centaur or a goblin, who thought that Hermione's birth was a sign of something significant in the magical world. They kidnapped her to study her or use her in their own cultural or magical practices. Or perhaps it was a wizard who had a grudge against Hermione's parents and took their child as revenge.
It could be a rogue vampire who wants Bella for her unique blood. There are many vampires in the Twilight world who might be tempted by her smell. Another potential kidnapper could be a vengeful werewolf who blames Bella for something, perhaps for the way the vampires and werewolves' relationship has changed. It might also be a human who has somehow found out about the vampire world and thinks they can use Bella to gain power or knowledge.
It could be a group of rogue demigods who are jealous of Percy's status and power. They might think that by kidnapping and torturing him, they can gain some of his abilities or just to prove that they are stronger.
It could be a group of rogue Death Eaters who want to use baby Harry as a bargaining chip against Voldemort. They might think that by having Harry, they can gain power within the dark wizard's ranks or even overthrow him.
The Sith could be potential kidnappers. They might see Princess Leia as a powerful Force - user and want to either turn her to the dark side or use her in some dark ritual. Another possibility is the bounty hunters. They could be hired by some powerful and shadowy figure to kidnap Leia for various reasons, like for political leverage or to get information from her. Also, a new and unknown alien race that has just entered the galactic scene could be the kidnappers. They might not understand the significance of Leia but kidnap her out of curiosity or because they misinterpret her actions as a threat.
A new, unknown criminal organization could be behind the kidnapping. They might have heard about Duke's potential and see him as a valuable asset. They could be planning to either brainwash Duke to join them or use his abilities to carry out their illegal activities.
The Akatsuki could be potential kidnappers. They are always on the lookout for powerful jinchuriki like Naruto to extract the tailed beasts from them. Orochimaru could also be a kidnapper as he is always interested in obtaining powerful bodies and Naruto's strength would be very appealing to him.
It could be a rival vampire clan. They might see the son as a threat because of his unique nature, being part human and part vampire. They may think that as he grows up, he could become very powerful and pose a danger to their own power and territory in the vampire world.
It could be a dark organization that has been secretly operating in the shadows. They kidnap Naruto because they believe he has some sort of connection to an ancient prophecy that they want to either fulfill or prevent, depending on their motives.
The Grimm could also be involved in an unusual way. Perhaps a new type of Grimm that has the intelligence to kidnap. They might be working with a human or Faunus villain who has some sort of control over them, and they take the character to an unknown location where the RWBY team has to face not only the Grimm but also the mastermind behind it.
One possible motive could be to use Hermione as a bargaining chip against Harry Potter. Since Hermione is his close friend, the kidnappers might think they can force Harry to do something, like give up a powerful magical item or valuable information.