It could be April. Since she's a human and often involved with the Turtles' adventures, she might be an easy target. Maybe the bad guys convinced Mikey and Donnie that April was in some way endangering them.
Another option could be Casey. He's also close to the Turtles. If there was some false information spread about Casey being involved in something dangerous or illegal, Mikey and Donnie might think they need to take him into custody by kidnapping him.
Perhaps a new character, like a mutant who has some special power that the villains want to get their hands on. They trick Mikey and Donnie into kidnapping this mutant so they can steal the power for themselves.
It could be that they were tricked into thinking they were helping someone. A villain might have convinced them that the 'kidnapped' person was a bad guy who needed to be taken away for interrogation. But as the story unfolds, they realize they've been used and have to find a way to make things right.
While Mikey and Donnie are the main focus, sometimes their older brothers Leo and Raph can also play important roles in the fanfiction. For example, they might be searching for the missing baby turtles, or they could be the ones who teach Mikey and Donnie important lessons when they finally reunite.
One interesting plot could be baby Mikey and Donnie getting lost in the sewers while exploring on their own. They have to use their wits and the little skills they've learned to find their way back to their brothers.
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.
Splinter might be the main helper. He has raised the Turtles, so he has experience with taking care of young ones. He could teach the other Turtles the proper way to hold baby Mikey, how to soothe him when he cries, and give them advice on how to keep him clean and healthy. Splinter's wisdom would be really important in this situation.
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.
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.
It could be Shredder. He's always been after the turtles.
In this kind of fanfiction, the creators usually play with the characters' original traits. Karai, with her ninja skills and her own motives, could either be an ally or an adversary to Dark Mikey. For example, they might be forced to team up against a common enemy, and during that process, they start to understand each other better. It's all about exploring the uncharted territories of their personalities and the possible dynamics between them.