It is one if the most complicated things that I have ever done. It is never finished, never perfected, but it is full of complications and great thought.
There have been multiple different versions. Each time the aim is to create something that invokes the same kind of emotions from the River Song storyline. Mystery. Emotional depth for the Doctor which we have experienced in different levels. The bond with his granddaughter, the impossible love he seemed to share with Rose, the kind of connection he shared with Jenny, at having someone he was bonded to on a flesh and blood scale after all this time. The River Song story was a whole other kettle of fish. We had mystery and shocks and complications, thrills and heartbreak and such incredible love we hadn't seen the Doctor experience on screen before.
Sophia is something of a combination of some of these events.
There are many different versions of Sophia's story, but always she is an artificially created human with the ability to think like the Doctor. In some versions, the Doctor truly cares for her and they have a sort of parent and child bond. There is no DNA connection, but she exists because of the Doctor, or the Valeyard, and certainly carries a great degree of the Doctor about her.
Right now I am focusing on the darker version. That the Doctor didn't want to regenerate, someone forced it to happen, he became the Valeyard, created Sophia, but the remnants of the Doctor's personality fought back to keep her safe from the Valeyard as a child. The Valeyard, pretending to be the Doctor, returned for Sophia when she was twenty one years old. He performs secret tests on her, such as seeing how she thinks and behaves in certain situations, then eventually reveals who he really is. He traps her, he performs experiments on her and tortures her. To the extent she actually tries to end her own life, but he saves her. And then Sophia finds a way to fight back and get help from the former companions, who help her bring back the Doctor. Sophia's whole existence is a massive paradox. She causes the regeneration of the Valeyard back into the Doctor and then later in her own personal timeline, forces the regeneration of the Doctor into the Valeyard, which causes her own creation as a result.
What makes this so terrifying is that usually it is the Doctor who prevents these situations. In most cases, he saves his companions from the worst case scenario. A lot of his companions walk away mentally or physically scarred in some way, but the Doctor usually intercepts before they're killed or badly hurt or mutilated. Companions like Bill Potts are the exceptions and that was pretty traumatising. In this case, it is the man who was once the Doctor who is doing these things to the companion. So who will save the day?
One of the complicated parts, asides from the fact this is the darkest piece of Doctor Who fanfiction I have ever written, was how to present Sophia as a character. She is smart. She's human. I wanted her to be a strong woman and not a victim. But I also wanted to emphasise how she is human. A human with intelligence and personality traits that make her wildly different from other humans. Getting the balance was tricky, especially as, for a huge part of it, Sophia has to be the hero character. She has to be the Doctor.
I wrote a brief episode plan for how things would play out if Sophia's story were to become a reality for the show. Early episodes would prove Sophia's intelligence, knowledge and wide skills. At least one would show how she is adept in self-defence and various martial arts and general fighting skills. Showing she's physically strong as much as anything else. An episode would show Sophia is also something of an escape artist with the ability to release herself from various restraints. Whether that's standard handcuffs or rope bindings. She can pick locks and knows how to get out of electronic locking systems, although she may need certain equipment (not a sonic device, I'm thinking more of how Luke Smith in Sarah Jane adventures opened doors by wiring the controls to a mobile phone). She also has a way of viewing people with suspicion and isn't great at trusting anyone immediately.
Except the Doctor. Sophia was raised by Kate, then Ace, essentially to be the Doctor's companion and he's the one person, outside of the circle of people who raised her, that she thinks doesn't need to prove she can trust him. Or, at least trust him to a certain extent. Kate knows from her own experiences, and her fathers, that the Doctor might hide things, or not be completely honest. Ace knew full well how manipulative the Doctor would be. Sophia's met just a few of the other companions too, who give her warnings. But they all make it clear that the Doctor would always do his utmost to keep them alive and would never actually harm any of them.
The only one who could really warn Sophia that the Doctor might become something else is Mel Bush, but there are two reasons why this wouldn't happen. One is that Mel never tells the story of the Valeyard to anyone on the basis that she never quite understood it and believed it was an averted or false future. The other is that Sophia met very few of the former companions prior to becoming a companion herself. Kate and Ace both agree that fewer people should know about Sophia until they know which Doctor left her and why. Therefore, asides from themselves and the Brigadier, the only former companions to really know anything are Sarah Jane Smith (who they ask for advice on account of her raising a son not so different from Sophia) and Martha, who is consulted for a medical view point.
So, inside the TARDIS, Sophia lets her guard down. The Valeyard has been paying attention. He knows how Sophia won't suspect him of trying to drug her. He knows exactly how to restrain her and make sure she can't escape. He knows how to keep her from attacking him. This is how he manages to trap Sophia and keep her imprisoned as his experiment.
Sophia's strong mental abilities hold out all the way. She fights back every time the Valeyard tries to see inside her head and throughout it all, she is secretly plotting a way to get out. She doesn't have a lot of options though. Her main choice is to simply keep fighting. She doesn't know what it is the Valeyard wants to gain from his experiments, but she knows one of the best things she can do is to ensure he doesn't get the information he wants, or he gets inaccurate information. The equipment the Valeyard uses, although it is sufficiently adapted to ensure she cannot escape, it is something she has seen before and understands. This means that she knows how to trick it. Additionally, she's also been subject to the Valeyard's psychic powers before and she knows how to block him.
So she deceives him into thinking he's found her pain threshold and manages to keep him from seeing the deepest parts of her mind.
I go back and forth on the idea that Sophia is to driven to the point of trying to end her own life. I think I wrote what I did when in a very dark place myself. I may revert back to another version where instead, Sophia appears to contemplate ending her life but is, possibly, only testing the Valeyard and his determination to keep her alive. It is important to have such a scene because this is supposed to invoke what remains of the Doctor from deep inside the Valeyard's consciousness, allowing her access to the memories of the Doctor without the Valeyard's knowledge.
What happens to Sophia after she brings back the Doctor? I think she may go on one last adventure to help this new Doctor find out who they are, but leave soon after. Perhaps after finding the Doctor's new companion and leaving, knowing they'll be OK, but still appears occasionally, or at least is mentioned, when the Doctor returns to Earth and meets with people from UNIT.
I wrote some scenes in which many of the former companions are captured alongside several different versions of the TARDIS. I had to try and balance Sophia being herself, showing signs of the Doctor and the companions also being pretty amazing without the Doctor. The recent versions show that Sophia has been working as a scientific journalist in America for a year and it hasn't been clear whether she is dealing with what happened to her or not.
Although Sophia is the first to escape her restraints and distract their captor, it is the other companions who, all doing their bit, restrain their captor and figure out how to solve the situation, not Sophia. This would, I think, bring her back into the field as a defender of Earth alongside the other companions and UNIT, using her scientific genius in a way she was always capable of, rather than living a quieter life in America. But for the sake of the TV show, if this ever did become a real thing (it won't), then Sophia would be absent for a lot of it as otherwise there would probably be a bit too much genius on screen.
The whole thing is very complicated and has been fun to write, even if it complicated and sometimes very dark.
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