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 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.
It could be an envious rival. Maybe someone who's always been in the shadow of Osomatsu and his brothers and decides to take matters into their own hands by kidnapping Osomatsu. Another option is a deranged collector. This person might see Osomatsu as a rare item to add to their collection of oddities. Or it could be a vengeful spirit. In a more supernatural setting, a spirit with a grudge against the Matsuno family could kidnap Osomatsu as a form of revenge.