A group of rogue shinobi who have a vendetta against the Hidden Leaf Village might be the kidnappers. They see Naruto as a means to get revenge on the village. They think that by taking away the son of the Fourth Hokage, they can cause great pain and disruption to the Leaf.
It could be Orochimaru. He is always on the lookout for powerful specimens to experiment on or train in his ways. Naruto, as the son of the Fourth Hokage, would be an extremely appealing target for him at birth.
Perhaps a mysterious and long - forgotten clan kidnaps Naruto at birth. This clan has some ancient prophecy or grudge related to the Uzumaki clan. They believe that by taking Naruto, they can either fulfill the prophecy in their favor or settle the old score with the Uzumaki and by extension, the Leaf Village.
It could be a rogue ninja who wants to sell Naruto to the highest bidder. There are always those in the Naruto world who are after power and money.
Well, it could be a secret organization that has been operating in the shadows. They might have some ulterior motive related to Naruto's power or his connection to the Nine - Tails. Maybe they believe that by kidnapping Naruto, they can control the Nine - Tails and use it for their own purposes. Another option is a jealous ninja from within Konoha. This ninja might feel overshadowed by Naruto's achievements and popularity and decides to kidnap him to get him out of the picture. Also, a powerful and ancient being awakened from a long slumber could be the kidnapper. They see Naruto as a source of energy or a key to something they desire.
Well, it could be an obsessed fan who wants to keep Naruto all to themselves in the fanfiction. Maybe they think Naruto has some special power they can use for their own gain.
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 an orc warband. Orcs have always been enemies of the elves, and they might see Legolas as a valuable captive either for ransom or to torture. Another possibility is a rogue wizard. Wizards who have turned to the dark side often seek powerful beings to experiment on, and Legolas, with his elven magic and skills, would be an interesting subject.
As mentioned before, Eggman is a likely candidate. He's always had his eyes on Tails' skills and would stop at nothing to use them for his evil plans. So he could be the one behind the kidnapping.
It could be a jealous rival. Maybe someone who has always been in competition with Shawn in some aspect of his life, like work or a hobby, and decides to take drastic measures by kidnapping him.
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.
It could be an envious rival. Maybe someone who's always been in the shadow of Osomatsu and his brothers and decides to take matters into their own hands by kidnapping Osomatsu. Another option is a deranged collector. This person might see Osomatsu as a rare item to add to their collection of oddities. Or it could be a vengeful spirit. In a more supernatural setting, a spirit with a grudge against the Matsuno family could kidnap Osomatsu as a form of revenge.
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.