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The Doctor's Wife
She had once vowed she'd never marry. An easy decision given her father's relationship with his wives. Divorced, beheaded, dead, divorced, beheaded, outlived. Not the best encouragement for pursuing marriage. Especially if it meant watching a husband be unfaithful and have to give up all her power.
Then she met the Doctor. She had heard whispers of him growing up, of his past involvement in her ancestor's lives. She had never thought he was real though, not until he showed up one day with that blue box of his.
It was right after a verbal fight with Mary who had told her she'd never amount to anything. That she was nothing but an illegitimate bastard who was the daughter of a witch and their father would never love. Harsh words to a young girl of seven years.
The gardens were her refuge, a place to dry her tears. Then he showed up—his hair was disheveled and she didn't recognize his clothes, but she did recognize the box. Without even asking her name, he pulled out a handkerchief and offered it to her. Gradually he coaxed the story of what happened out of her, and when she told him her name, he did something unexpected.
He brought up her chin and met her gaze. Eye to eye, he said in the most serious all knowing voice, "Don't cry, you're somebody, alright. You're the Great Queen Bess, ruler of England in what will be known as the Elizabethan era, a great time to be in England. Future queens, great queens, will be named in your honor. Your father may have wanted a son, but he got the best daughter he could ever ask for."
She didn't understand his words completely. Her, being queen? There was still Edward and Mary, and technically, she couldn't even inherit the throne. But he was so confident, and that smile of his was contagious so she smiled too.
The next time she saw him, she was indeed a queen. She was also older and had been hoping for his return for a long time. Her other suitors could offer her great wealth, but the Doctor could offer her all that and more—all of time and space, a chance to not be a ruler for a short while. Furthermore, he didn't see her as a weak woman or a prize, but as a friend and genuinely cared for her.
The incident with the Zygons scared her greatly. Not just the thought of losing her country to the foreign creatures, but her life and the Doctor's as well. That's why she insisted on marrying him, that way he'd be connected to her forever. Even with everything going on, she'd never been happier.
Then he left, giving her instructions on what to do with the Zygons and their portraits and of the letter she was supposed to write. Ever the faithful and dutiful wife she did so. And she waited.
She waited. Sometimes earlier versions of him would show up, and she'd have to pretend to not know him. It was so hard, but she did remember him stressing the important of paradoxes and the Doctor knowing things before he should.
Once she came so close. She heard rumors about a strange man with a strange companion helping out Will Shakespeare. She immediately cleared her schedule to visit the next performance at the Globe, hoping it was version of her husband who knew who she was. By the time she got there, he was running away from her.
That could have to do with her calling him a sworn enemy, but how else was she to inform the guards about his importance? The few who knew of their marriage had been sworn to secrecy. Her relationships with France and Spain were on shaky ground as it was, who knew what'd they do if they found out her hand in marriage was no longer an option. Alright, she may have said it in a bit of anger, but what wife wouldn't be angry when her husband had been away for years, never sending word?
So, she continued being the dutiful and faithful wife and waited for her husband to return to her, eventually earning the name the 'Virgin Queen'. The name wasn't accurate, but it might as well be.
In the end, her husband didn't leave her for another woman or because she failed to give him an heir. The Doctor was a better man than her father was. Instead, he left her for the universe. Why be the King of England when you could be the Lord of Time and Space? If only he'd ask her to join him—she would have said yes.
As she grew older and he didn't return, she became less of the lovesick girl she had once been. She ruled as the Good Queen Bess he had once told her she would be. She also tried her best to be ruler her people needed her to be, putting her personal feelings aside. She made sure that was how history would remember her, the strong Queen who provided her people with stability and security rather than the foolish girl who would have run away with her husband, a madman, if he had only asked.
History may have known her as Elizabeth I, Queen of England, but she would always think of herself as something else first—the Doctor's wife.
This was written spur of the moment, so if I got any historical or Dr. Who facts wrong please forgive me. I haven't written anything in a while, but I felt like Moffat's portrayal of Elisabeth I was wrong. She's always portrayed as a strong ruler, not some lovesick girl who's obsessed with the Doctor. The best I could figure was that his Elisabeth was young and just became queen, and the Doctor had made quite the impression on her once. Then as she got older, and the Doctor stopped visiting her, she became less of the girl she had been and more of the woman history remembers her.