It could be an old acquaintance from his past who has turned to the dark side. Maybe someone he once trusted during one of his earlier adventures but who has since become jealous of Drake's success and wants to use him to get rich quick. For example, a former partner who was left behind in a previous treasure hunt and now blames Drake for his misfortunes.
A powerful and wealthy collector of rare artifacts might be the kidnapper. This person has heard of Drake's reputation for finding treasures and believes that he can lead them to a particular item that they've been desperate to add to their collection. They think that by kidnapping him, they can force him to reveal the location.
In a fanfiction, the kidnapper could be a cult leader. The cult believes that Drake has a connection to an ancient prophecy or power. They kidnap him in order to use him as a sacrifice or to extract the knowledge they think he has. They might have been following his adventures for a long time and finally see an opportunity to get their hands on him.
One plot idea could be that Nathan Drake is kidnapped by a long - lost rival who believes he has the key to a hidden treasure. The rival takes him to a remote island. Drake then has to use his wits and knowledge of the area's history to escape and turn the tables on his captor. He might find clues within the kidnapper's lair that lead to a greater mystery.
Maybe it's a criminal mastermind that Drake has been getting too close to in his investigations. This person sees Drake as a threat and decides to kidnap him to halt his progress. It could be someone who has a lot to lose if Drake exposes their illegal activities, like a powerful underworld figure running a large - scale smuggling operation.
Well, there's a fanfiction called 'Nathan Drake and the Ancient Artifact'. It has a really engaging plot where Nathan is on a race against time to find a powerful artifact. Then there's 'Nathan Drake's New Allies' which shows him teaming up with some unexpected characters. Also, 'Nathan Drake: Beyond the Maps' is quite good as it explores uncharted territories that the game might not have covered.
It could be Dr. Eggman. He's always after Sonic and would love to get his hands on him to stop Sonic from foiling his evil plans. He might want to study Sonic's speed and use it for his own machines.
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.