In this fanfiction, it could be that the kidnapping was a setup by a bigger villain to lure the other Turtles into a trap. Mikey is just the bait. The other Turtles then have to use their wits and skills to not only rescue Mikey but also avoid the larger danger that awaits them. They might discover new allies or powers along the way as they try to save their friend.
Well, perhaps the kidnappers think Mikey has some special knowledge or power. So they take him to try and extract that from him. But in reality, Mikey doesn't have what they think he does, and he has to figure out how to convince them before they do something drastic.
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 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.
Well, perhaps a new villain who has heard of Donatello's genius kidnaps him to use his brainpower for some evil scheme in the underworld. Donatello might be able to use his wits while in captivity to leave clues for his brothers. And his brothers, once they realize he's missing, would start scouring the city, interrogating informants and following leads to find him.
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.
A plot twist could be that the place where the character is kidnapped has some hidden objects or clues that can only be found without glasses. For example, there might be a hidden message written in a way that is visible only to blurry vision. Also, the character might be kidnapped by someone they thought was a friend, and without their glasses, they initially mistake the kidnapper for someone else, which adds to the mystery and confusion. When they finally realize who it is, it's a big shock.
One possible plot twist could be that Sasuke was actually being controlled by an unknown enemy when he kidnapped Hinata. This enemy might be using Sasuke's power to get to Naruto through Hinata. Another twist could be that Hinata has some hidden power or knowledge that Sasuke's side needs, and the kidnapping is a way to extract that from her. Maybe it turns out that Hinata was expecting the kidnapping all along as part of a larger plan to infiltrate Sasuke's group and learn their true intentions.
It could be Shredder. He's always been after the turtles.
One possible plot twist could be that Red X has a hidden agenda that's not actually malicious towards Robin. Maybe he's trying to protect Robin from a greater threat that the Teen Titans are unaware of. For example, there could be a new super - villain in the city who is targeting the Titans, and Red X believes that by taking Robin, he can keep him safe until the danger passes.
One possible plot twist could be that Itachi has been mind - controlled to kidnap Sakura. Maybe an enemy of Konoha has a powerful jutsu that forces Itachi to do this against his will. Another twist could be that Itachi kidnaps Sakura as a means to protect her from a greater threat in the shinobi world that no one else is aware of yet. He might know that she has some sort of power or knowledge that makes her a target, and by kidnapping her, he can keep her safe in a hidden location.
A great plot twist could be that Orochimaru is not acting alone in kidnapping Female Naruto. There could be a secret alliance between him and some other powerful and shadowy figures in the ninja world. These figures might be pulling the strings and have their own plans for Naruto. As she is held captive, Female Naruto discovers that there is a prophecy about her that she was not aware of, and this prophecy is what makes her so valuable to Orochimaru and his allies. She then has to figure out how to break free and stop whatever evil plans they have in store for her based on this new knowledge.