There's a possibility that it's a super - villain who has been waiting for the right moment to strike. Tony being in Siberia gives the villain a chance to isolate him from his usual support system. This villain could be someone with a vendetta against Tony, perhaps someone whose plans were thwarted by Tony in the past and now wants revenge by kidnapping him.
It could be a terrorist group. They might see Tony as a valuable target because of his wealth and technology.
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.
Perhaps in this fanfiction, Tony is kidnapped from Siberia by a powerful villain who has a long - standing grudge against him. The kidnapper could be after Tony's Iron Man suit technology. They snatch him from Siberia as it was a place where he thought he could be safe or was conducting some top - secret research related to his suit's power source. His friends then have to embark on a dangerous rescue mission.
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.
Maybe he uses his magic. Loki is a powerful sorcerer. He could have created a portal or used some sort of teleportation spell to get to Siberia quickly.
It could be Dr. Eggman. He's always after Sonic and would love to get his hands on him to stop Sonic from foiling his evil plans. He might want to study Sonic's speed and use it for his own machines.
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.