Maybe a rogue mutant. There are all kinds of mutants in the TMNT universe. One that has a grudge against the Turtles or just wants to use Donatello's skills for their own gain could be the kidnapper.
Another possibility is a human scientist who has gone mad with power. He might have been studying the Turtles from afar and decided that Donatello's technological know - how could help him achieve his insane goals. So he devises a plan to kidnap Donatello and force him to work for him.
It could be the Foot Clan. They've always been enemies of the Turtles, and kidnapping Mikey would be a way to get back at them or gain some advantage.
Well, perhaps a new villain who has heard of Donatello's genius kidnaps him to use his brainpower for some evil scheme in the underworld. Donatello might be able to use his wits while in captivity to leave clues for his brothers. And his brothers, once they realize he's missing, would start scouring the city, interrogating informants and following leads to find him.
It could be Shredder. He's always been after the turtles.
It could be a terrorist group. They might see Tony as a valuable target because of his wealth and technology.
It could be an old enemy of Keith's, someone from his past who has a vendetta against him. Maybe a former rival from his days in the military academy who has now turned to more devious means.
In some creative fanfiction, it could be an alternate version of Spiderman himself from a different dimension. This Spiderman has gone bad and kidnaps a fan from our dimension as part of some grand, dark plan that involves crossing dimensions and causing chaos.
A power - hungry nobleman from a neighboring land could be the kidnapper. He might believe that by having Rapunzel in his possession, he can gain some sort of political advantage or use her as a bargaining chip against her kingdom.
It could be Orochimaru. He's always been interested in obtaining powerful individuals for his experiments, and Naruko with her unique abilities would be a prime target.
It could be a new villain that has emerged, someone who is jealous of Gohan's power and wants to make it his own. This villain might be from a far - off planet and has heard of the Saiyan legend.
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.