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.
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.
It could be Shredder. He's always been after the turtles.
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.
In a fanfiction, Mikey might get hurt during a mission to infiltrate a Kraang base. He could be detected by security systems and get zapped by some sort of electric defense mechanism. This would leave him weak and in pain. His brothers would need to carry him out of there and find a way to reverse the effects of the zap. They'd be desperate to get Mikey back to his normal, energetic self.
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.
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.
In such a fanfiction, Tails might be kidnapped by an old enemy like Dr. Eggman. His friends, like Sonic, would then start a rescue mission. They would search all over the place, from the Green Hill Zone to Eggman's secret bases.
Well, his friends might launch a rescue mission. They would use their various skills to track down where Kakashi is being held. Naruto could use his shadow clones to search different areas, while Sasuke might use his Sharingan to detect any hidden threats on the way to the rescue.
In such a fanfiction, Goku might be kidnapped by a powerful new villain. His friends would then start a search mission. Maybe Vegeta would be the first to volunteer, thinking it's his chance to prove he's stronger than Goku.