It could be Shredder. He's always been after the turtles.
The Kraang could also be the kidnappers. They might want to study Mikey for some of their evil experiments.
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, 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.
I'm not sure specifically as I haven't read this particular fanfiction. But it might be about Mikey from the Teenage Mutant Ninja Turtles getting some sort of skin condition like shellacne. It could involve his friends helping him deal with it, or his own journey in handling this new and unexpected situation.
He might gain new physical abilities, like enhanced strength or speed.
April and Casey might also be part of this fanfiction. April could use her reporting skills to try and figure out what's going on with Mikey's mutation, and Casey would be ready to fight any new threats that come along because of Mikey's changed state. Also, Splinter, as their sensei, would be guiding them all through this difficult time, providing wisdom and training to help Mikey control his new powers if he has any.
In this fanfiction, Mikey might gain new and unexpected powers. Maybe he could develop the ability to control certain elements like water or fire, which would add a whole new dynamic to his character and the story.
Maybe it's a group of poachers who are after rare Pokémon. Gengar, being a relatively unique and powerful ghost - type, would be a valuable catch for them. They could plan to sell Gengar on the black market for a high price.
It could be the Joker. He's always up to no good and kidnapping Robin would be a great way to mess with Batman. The Joker might want to use Robin to force Batman into a series of cruel and twisted games.
Maybe an enemy from another village. If there are political tensions between villages, kidnapping Sarada could be a way to gain an advantage. They might think that by having her, they can force her village to make concessions in treaties or resources.
It could be a new villain who has heard about Tails' mechanical skills. This new baddie might think that by kidnapping Tails, they can force him to build powerful weapons for them.