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.
Maybe it's a new villain that we haven't seen before in the TMNT universe. This villain could have a special grudge against Mikey specifically, perhaps because of something Mikey unknowingly did in the past.
It could be Shredder. He's always been after the turtles.
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.
Well, his brothers would probably go on a wild rescue mission. They'd search every nook and cranny of the city. Maybe they'd get some help from April and Casey too.
One possible plot twist could be that Mikey was kidnapped by an unexpected enemy, like a former ally who turned bad. Maybe it was someone he trusted, and this betrayal adds a layer of drama.
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.