"Who?" Clara asked, puzzled. She'd never heard the Doctor mention the name Madame Kovarian before, and yet he was acting like it was something horrifyingly familiar.
He was sitting on the floor now, legs crossed in front of him with his arms balanced against them. His gaze was unfocused ahead of him, looking into the past in places often too sorrowful for him to go. But he had to explain, no matter how it hurt him.
"A long time ago…when I was traveling with the Ponds…she was the one who managed to kidnap Amy Pond when Amy was pregnant with Melody Pond—that's River Song's true name. When Amy gave birth, Kovarian took the child and programmed her to kill me. River grew up with one goal—to someday be my assassin. However, through a twist of timey wimey circumstances, she managed to grow up alongside her own mother and father; and Amy instead inculcated in River a kind of infatuation for me. I've told you before that River and I met out of sync with each other; River at times wanted to kill me and at others adored me." He took a deep breath and continued. "I wound up marrying her to restore time to its normal function. The last time I saw her before this circumstance, was at Trenzalore, when you jumped into my time stream. She was already dead then."
Clara shifted in her chair. "But what about Madame…Ko-Ko-whatever her name was?"
Her question broke his reminiscence about River's past. "Yes. Kovarian was a member of a chapter of the Church of the Mainframe that broke away from the main church and joined forces with others to try to kill me. They made several attempts. I had thought her killed during the aborted timeline where I married River…but I was wrong." He shivered involuntarily.
Clara shivered too, and realized it was a bit chilly in the house. She stood up and held her hand out to the Doctor. "Come on…let's go in the kitchen, and I'll heat up the kettle again for tea. You can tell me the rest in there." He took her hand and she helped him up.
The two settled down at the kitchen table with steaming mugs and a plate of jammie dodger biscuits, and the Doctor continued his tale.
After kissing River and then collapsing he didn't remember much, except being moved about and then finally coming fully to on an examination table in a sterile room. River was standing nearby, and walked over to him once she noticed he was aware again of his surroundings. Apologizing once more, River told him Kovarian had blackmailed her into capturing the Doctor using one of her trademark lipsticks. Kovarian had threatened to outright kill the Doctor if River hadn't cooperated. The whole incident with the stolen diamond had been a ruse to try to lure the Doctor into her orbit, and then deliver him to Kovarian. When he'd asked why Kovarian hadn't had him outright killed, River stated that the Silence wanted to harvest samples of his physiology before exterminating him. It seemed that branch of the Church was low on funds, and certain interested parties would gladly give heavy donations in return for any part of his Gallifreyan anatomy that they could exploit medically.
River helped him up, telling him she was going to double-cross Kovarian, and get him reunited with the TARDIS so they could make an escape off of the spaceship they were presently trapped on. She'd been planning this for some time, and she and the Doctor almost accomplished their getaway when Kovarian cornered them.
A battle ensued, and the two managed to make it to a narrow gantry way with Kovarian hot in pursuit. As they reached safety, River shot the support tethers for the gantry way, and Kovarian and her Silence henchmen fell to their apparent deaths into the ship's reactor. The Doctor and River made it to the TARDIS and took off.
The Doctor then asked River if she was interested in going back to Darillium to continue their date. River refused; she felt he was doing it out of pity. She told him she had another obligation—she was leading an archaeological expedition into a planet-wide library paid for by the Lux family. He took her to the meeting point for her expedition team, and parted with her there.
When he returned to the TARDIS, he started feeling the full effects of the poison. Unknown to River, the hallucinogenic lipstick she'd used on him had actually been a fatal poison. Madame Kovarian most likely had switched lipsticks on her at some point, and River had unknowingly given him a kiss of death on Darillium. It was slow acting, which accounted for why, even though he'd escaped with River, he hadn't felt one hundred percent himself since the moment her lips had touched his. Alone in his TARDIS, he'd programmed it to materialize on Clara's roof after coming out of the vortex. He recorded his final message as the surly Scot, pulled the lever to escape the vortex, and then regenerated.
"So…now what? Will you join up with River on her archaeological dig? Now that you know she wasn't really trying to kill you, I'd think you'd want to get back together," Clara speculated, staring into her mug. She felt curiously empty inside after hearing his tale.
"Clara…River is dead now. Darillium is the last place she and I were together at. The Library is where I first met her in my tenth incarnation…and where she last saw me. She was killed there, saving my life and the lives of thousands of other people trapped in the Library. As I told you before, the River you met the first time we went to Trenzalore was already dead. She was a data ghost. Not a person of flesh and blood like you and I." His eyes locked with hers, and Clara shivered a little. There was something very intense behind those green orbs.
"Well, can't you go back into her past and see her there? Or won't she show up again in the future? It…it can't be over…I mean, she's your wife after all," Clara stammered. "Surely you must miss her…"
He released a heavy breath, and looked down at his mug. "Yes and no," he replied. "I miss the good times I had with River. I mean, she loved me very much, and I had a very deep affection in return for her. But…I couldn't trust her. She had been programmed to kill me after all, and there were times I felt unsafe when she was around. Plus she had a habit of acting superior around me…like she knew more than I did. Me! The Time Lord! The Gallifreyan! And she was just a human. She was a special human, owing to her being conceived in the time vortex while on the TARDIS. But she was a human nonetheless. She was clever, sophisticated and sensual, so she had definite appeal; but she was also duplicitous, conniving and faithless as well. For all her going on about how much she loved me, she was certainly quick to find other husbands when given half the chance."
"Were you flattered that she bragged about how much she loved you?" Clara asked, remembering how irritated she herself was when River had acted condescending towards Clara during the "conference call" she was involved in with Madame Vastra, Jenny and Strax before the first time she found herself on Trenzalore. She'd twitted Clara unmercifully about not knowing the Doctor's true name. Clara now knew not only that about the Doctor, but his nickname from when he was in school on Gallifrey ("Theta") and what his first face had looked like, all the way through to his repeat performance with this face. She probably knew far more now about the Doctor than River had ever known. Not, she thought sadly, that it made much difference to him.
"Well, yes, in a way," he answered. "I mean, who wouldn't be? She went on about it in detail when we first got into trouble this last go round. How it's like loving the stars themselves and how you don't expect the sunset to love you back."
"Oh, my. I'm sure that pandered very well to your ego," Clara laughed. "You even memorized the very phrases. I'll bet she didn't know it was you when she said it, knowing how you soak up praise every chance you get."
He frowned at her. "If I deserve it I don't see why not."
"You are a conceited little brat! I don't know how any of us withstand you," she was giggling heartily now at his pomposity. The Doctor on the other hand was becoming more irritated. "Clara!" he remonstrated.
"All right, all right, I'll back off," she snickered. Gaining control of her laughter, she asked him the other question that had been burning in the back of her mind. "So…I understand the back story of how you came to be here last night. There's one more thing I want to know…why. Why did you change back to your previous face?"
