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.
One possible plot could be that during the regeneration process of the 9th Doctor, something goes awry with the Time Lord's normal regeneration cycle. Maybe there's interference from an outside force, like a powerful alien entity that wants to disrupt the natural order. This interference causes the regeneration to skip a few incarnations and directly jump to the 11th Doctor. The new 11th Doctor then has to deal with the after - effects of this abnormal regeneration. He might have some strange memories or abilities that are a mix of what the 9th Doctor was supposed to pass on and some new, unexpected elements.
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.
There's also a chance that a new, original villain could be created for this fanfiction. It could be an alien race that has a grudge against the Doctor for something she did in the past (even if it was a past regeneration). And they target Amy and Rory to get to the Doctor. This new villain could have unique powers and a complex backstory that makes them a formidable foe.
They could also meet in a time - locked situation. The 12th Doctor is trying to solve a mystery from his past, and the 13th Doctor stumbles upon the same situation in her present. At first, they don't understand how they are both involved, but as they start to piece things together, they discover that it's all part of a much larger, more sinister plot. Along the way, they might meet some old friends or foes from their respective tenures as the Doctor. And in the end, they work together to outwit the mastermind behind the plot, all while having some really interesting conversations about their experiences as the Doctor.
In the fanfiction, the 11th doctor, with his eccentric and energetic personality, could initially be a bit confused by the 13th doctor's more modern approach. But then they could start to combine their wits. For example, the 11th doctor's knowledge of ancient alien races could be paired with the 13th doctor's understanding of current galactic politics. They could work together to save a planet that is on the brink of destruction due to a complex web of time - related issues. The encounter could also lead to some humorous moments, like when they argue about who has the better sonic screwdriver or who has had the more exciting adventures.
In fanfiction, when the 13th Doctor meets the 11th Doctor, there could be a lot of chaos and fun. They might exchange stories about their adventures. Maybe they would team up to fight a common enemy that spans across their different timelines.
In fanfiction, when the 11th Doctor meets the 12th Doctor, there could be a clash of personalities at first. The 11th is so full of child - like wonder and the 12th is a bit more reserved. But then they might find common ground in their love for the TARDIS and for saving the universe. They could end up learning from each other. For example, the 11th Doctor might teach the 12th how to be more carefree sometimes, while the 12th Doctor could show the 11th how to be more strategic in dangerous situations.
In a fanfic, when the 10th doctor clone meets the 11th, it could be a moment full of drama. The 10th doctor clone, having his own set of memories and experiences, might initially be a bit hostile towards the 11th. But as they start to interact more, they could discover that they have more in common than they thought. For example, their love for adventure and their sense of justice. They could also compare their different TARDIS interiors and time - traveling techniques. Eventually, they might even form an alliance to protect the universe from a greater threat that neither could handle alone.
The main character would surely be the 10th Doctor himself. His companions, depending on the era, like Rose Tyler or Martha Jones, could also be main characters. They play important roles in how the Doctor adjusts to his new form.
The main characters are, of course, the 11th Doctor and Rose. The 11th Doctor is known for his energetic and somewhat eccentric personality. He has his signature bow tie and fez. Rose, on the other hand, is a strong - willed and adventurous character. She has her own set of skills and experiences from her previous travels with the Doctor.