The Cybermen could also be main antagonists. They might be converting the inhabitants of a planet that the Doctor and Romana are visiting, and the two have to stop them from spreading their cybernetic influence further. The Cybermen's cold, logical approach to 'upgrading' all life forms makes them a formidable foe.
Sometimes, original villains created specifically for the fanfiction can be the main antagonists. For instance, a shadowy figure who has the ability to manipulate time and space in ways that the Doctor has never seen before. This villain could be trying to rewrite history for their own malicious purposes, and Romana and the Doctor must work together to stop this from happening.
Often, the Daleks can be antagonists. Their goal of universal domination clashes with the Doctor and Romana's efforts to protect the universe. They might be trying to steal a valuable technology or resource that the Doctor and Romana are safeguarding.
One interesting plotline could be their exploration of a strange and uncharted planet. They might encounter unique alien species and have to solve puzzles to survive. For example, they find a civilization that has a very different concept of time, and the Doctor and Romana have to adapt to it while also trying to figure out how to get back to their own time and place.
It could be the Daleks. They are a classic Doctor Who villain. They might see the meeting of two Doctors as a threat to their plans for universal domination and try to stop it.
A group of corrupt politicians within the village itself could be the main antagonists. They might be secretly plotting to undermine Naruto's authority as the 5th Hokage in order to gain more power for themselves. They could be making deals with other villages or ninja groups that are not in the best interest of Konoha, and Naruto has to expose and stop their schemes.
The main antagonists could be the Death Eaters still loyal to Voldemort. They would be trying to undermine Harry and Ginny's efforts to protect Hogwarts and the wizarding world.
In some fanfictions, it could be the Death Eaters still causing trouble. They might be targeting Harry and Hermione specifically during their 6th year, trying to disrupt their studies or even harm them.
Well, usually the 11th doctor dark fanfiction has elements like mysterious and dangerous situations, moral dilemmas, and a departure from the typical heroic image of the doctor. It might also explore deeper psychological aspects of the character.
The Daleks could be the main villain. They might be trying to manipulate the Doctor's regeneration to create chaos in the time - space continuum. Since the 9th Doctor's unexpected jump to the 11th Doctor disrupts the normal flow, the Daleks could take advantage of this instability to further their evil plans of universal domination.
There could also be some characters from the Doctor's universe who oppose the idea of a half - wizard, half - Time Lord. They might come to the wizarding world to try and stop Harry from using his combined powers, fearing it could disrupt the balance between the two universes.
Well, it varies in different fanfics. The 11th Doctor could be hurt by powerful villains, or maybe in trying to save someone. It could also be from internal conflicts or emotional stress.
It could be due to various imaginative plot devices created by the fanfiction author. Maybe in a battle with a powerful villain or during a risky adventure.