It could be a disgruntled former employee. Maybe someone who felt underappreciated by Stark Industries and decided to take revenge by kidnapping Tony. Another possibility is a new super - villain who wants to make a name for themselves by taking on Iron Man. They see kidnapping him as the perfect way to get attention.
Perhaps a secret organization that has been observing Tony's work for a long time. They realize the potential of his technology and decide to kidnap him to force him to work for them exclusively. Or it could be a time - traveling enemy from the future who knows how important Tony will be in future events and tries to stop him by kidnapping him in the present.
It could be Hydra. They've always been after Tony's technology and his influence. Maybe they see an opportunity to get an edge over the Avengers by kidnapping him.
It could be a terrorist group. They might see Tony as a valuable target because of his wealth and technology.
One plot could be that a powerful enemy kidnaps Tony Stark to steal his Iron Man technology. They hold him in a secret lair and try to force him to reveal all the secrets of his suits. Another could be a fan with an extreme obsession who kidnaps him, thinking they can make him see things their way. Maybe they want him to create a special weapon just for them.
The Avengers would be in a state of panic and fury. Captain America would likely lead the charge to find Tony. He'd use his military strategy skills to plan a rescue mission. Thor might use his godly powers to track down any signs of Tony's whereabouts. Black Widow and Hawkeye would be on the lookout for any Hydra agents or informants. Hulk could be a wildcard. He might be uncontrollably angry and ready to smash anything in his path to get to Tony.
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.
It could be Zeref. Since Zeref has an interest in powerful magic users and Natsu is a strong dragon slayer, Zeref might kidnap Natsu to study his magic or use him in some dark plan related to his quest for immortality or power.
It could be an orc warband. Orcs have always been enemies of the elves, and they might see Legolas as a valuable captive either for ransom or to torture. Another possibility is a rogue wizard. Wizards who have turned to the dark side often seek powerful beings to experiment on, and Legolas, with his elven magic and skills, would be an interesting subject.
As mentioned before, Eggman is a likely candidate. He's always had his eyes on Tails' skills and would stop at nothing to use them for his evil plans. So he could be the one behind the kidnapping.
It could be a jealous rival. Maybe someone who has always been in competition with Shawn in some aspect of his life, like work or a hobby, and decides to take drastic measures by kidnapping him.
It could be a group of rogue Decepticons who are acting on their own. They might not follow Megatron's orders but still see value in kidnapping Arcee. Maybe they have a personal vendetta against her or think they can get rich by selling her to the highest bidder in the Cybertronian underworld.