Maybe it's a new villain in the detective - thief world. This villain wants to make a name for themselves by taking on both Kaito and Shinichi at the same time. They might be very cunning and have planned every detail of the kidnapping carefully.
It could be a secret society that has been observing their actions and sees them as a threat to their hidden agendas. This society might have members with special skills and resources to carry out the kidnapping.
It could be a criminal mastermind who sees Shinichi as a threat to his illegal activities and Kaito as someone who can be used as leverage. Maybe a powerful underworld figure who has been on Shinichi's radar for a long time and decides to take action by kidnapping them both.
Another potential kidnapper could be a new villain that we haven't seen in the official Ninjago series yet. A fanfiction gives the writer the freedom to create a whole new antagonist who has a special grudge against Lloyd or wants something that only Lloyd can provide.
In such fanfiction, Shinichi is often depicted as still having his sharp detective mind. He's intelligent, observant, and tenacious in solving problems. Kaito, on the other hand, is shown as his flamboyant self, with his amazing skills in magic and disguise. He's also quite charming. Both of them might have a bit of a competitive streak towards each other, which adds to the tension and interest in the story.
It could be Orochimaru. He's always been interested in obtaining powerful individuals for his experiments, and Naruko with her unique abilities would be a prime target.
It could be a new villain that has emerged, someone who is jealous of Gohan's power and wants to make it his own. This villain might be from a far - off planet and has heard of the Saiyan legend.
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.
Maybe it's a group of villains working together. They could be from different factions but united by the idea that Izuku has the potential to become a huge threat to their plans. They might kidnap him to either eliminate him or turn him to their side. Also, it could be a lone, obsessed fan of a villain who wants to prove themselves by bringing Izuku to their idol.
A group of outcasts from different islands might kidnap Moana. They feel that they have been wronged by the 'normal' society that Moana represents. They hope that by kidnapping her, they can get the attention they deserve and force the islands to change their ways. But Moana listens to their grievances and tries to find a way to help them while also finding a way home.
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 a jealous rival from his own village. Maybe someone who is envious of Shikadai's natural talents and popularity, so they decide to kidnap him to get him out of the way.