Well, there could be all sorts of twists. Maybe the kidnapping is part of a larger conspiracy involving other alien races or time-traveling villains. The Doctor would have to use all their wits and gadgets to save the day.
In such a fanfiction, the kidnapped person might hold a key to some ancient secret or have a special ability that the kidnappers want to exploit. The Doctor's journey to free them could take them to unknown corners of the universe and introduce new allies and enemies along the way.
Well, she might be held for ransom. Maybe the kidnappers think that as a nurse, she has access to valuable medical information or drugs that they can sell on the black market.
In this fanfiction, the 12th Doctor might face all kinds of adventures and challenges while being kidnapped. It could involve his companions trying to rescue him and uncovering a big conspiracy.
The story might involve a complex plot where the kidnappers have some sinister motive, and the Doctor has to use his wits to escape.
It could lead to all sorts of interesting plot developments. Maybe there would be challenges related to protecting the baby in the midst of time-traveling adventures.
It varies! Sometimes Clara is held for ransom, and the Doctor has to negotiate. Other times, it's part of a larger conspiracy and Clara's kidnapping is just the tip of the iceberg.
It could lead to a wild adventure as his companions race to save him. Maybe there's a villain with a specific motive behind the kidnapping.
It could be a rival spy agency. They might see Moneypenny as a valuable target to get information about MI6's operations. They would likely be highly trained and well - equipped.
Maybe it's a character from one of the games Matpat has theorized about. For example, if he made a theory about a game villain being more complex than thought, that villain could come to life in the fanfiction and kidnap him to prove his own power and intelligence.
The kidnapper might be a deranged Toad. Maybe this Toad has been corrupted by some evil force and decides to kidnap Luigi for reasons only known to the twisted mind of this new 'evil Toad'.
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.