Perhaps an old enemy of Igneel, Natsu's dragon father. They might see Natsu as a way to get revenge on Igneel. They think that by torturing Natsu, they can somehow hurt Igneel even though he's not around. Or it could be a group that is after the secrets of dragon slayer magic and believe Natsu has the key to unlocking those secrets.
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.
One possible kidnapper could be a rival engineer who is jealous of MacGyver's fame and ability to solve problems so effortlessly. This person might think that by kidnapping MacGyver, he can steal his ideas and take credit for his inventions. Also, it could be a group of eco - terrorists who believe MacGyver's work has been harmful to the environment in some way and want to force him to make amends by using his skills for their cause. A third option is a deranged fan who has an unhealthy obsession with MacGyver and wants to keep him all to himself, thinking that kidnapping is the only way to have MacGyver's undivided attention.
Perhaps a dark guild that has been observing Fairy Tail for a long time. They see Mirajane as a valuable asset and believe that her powers can help them in their evil plans. So they plot to kidnap her and force her to cooperate.
Another possibility is some disgruntled former employees. Maybe they feel they were wronged by Stark and want to get revenge. They know his routines and weaknesses well enough to plan a successful kidnapping.
One possible motive could be to gain power. Natsu is a Dragon Slayer, and his magic is very powerful. The kidnappers might want to extract his magic or use him as a weapon. Another motive could be for revenge. Maybe Natsu has unknowingly wronged someone in the past, and they are out for vengeance. Or perhaps they are working for a greater evil, and Natsu is seen as a threat to their plans, so they want to get rid of him by kidnapping him.
It could be a group of rogue shinobi from a neighboring village who are jealous of Konoha's power and see Hinata as a valuable hostage. They might think that by kidnapping her, they can gain some leverage over Konoha in terms of resources or territory.
A powerful and vengeful warlord from a forgotten realm could be a kidnapper. He might see Wonder Woman as a threat to his plans of conquest and decides to take her out of the picture by kidnapping her.
Perhaps it's a group of bandits who don't really understand who Mikasa is. They just see her as a valuable hostage to get what they want from the military or the local communities. They might be after food, weapons, or just a large sum of money in exchange for her safe return.
It could be a rival ninja clan if this is in a ninja - themed story. They might see Sakura as a valuable asset to get information about her own clan or to use her skills against her people.
A new, evil sorcerer who has just arrived in Narnia could be the kidnapper. He might have heard tales of Lucy's importance and figure that by taking her hostage, he can control the forces of good in Narnia. Or perhaps a tribe of wild centaurs who have been corrupted by some dark magic might kidnap Lucy. They could be under the influence of a spell that makes them believe Lucy is the cause of all their problems and that getting rid of her will solve everything.