He led them back to the TARDIS and found the control room to be deserted; presumably the older Ponds were putting Carys to bed. He was relieved.
By the time Jack and Sophia entered the TARDIS, the Doctor was already fiddling with the controls on the console. He wanted to start scanning Sophia as soon as the TARDIS could.
"Love what you've done with the place," Jack said in awe of his new surroundings. Sophia said nothing but quietly observed her environment and sat down near the console. It wasn't long until Jack joined her, looking quite at ease.
The Doctor was growing impatient. He knew the DNA scan would take time; however, he wanted the results quickly so that he could have his questions answered. Finally there were results and he could see it quite clearly. Sophia's genetic drift was consistent with her being descended from him, with the unique factor that there were also strands of human DNA mixed with Timelord.
His stare between his scanner and her face was enough for Sophia to realize the results were in. "Satisfied," she said with a small smile on her face.
"How are you possible?"
"Long story." He didn't look impressed so she stood up and thought a few moments before continuing. "You left Susan with David Campbell in the twenty-second century they fell in love, and eventually wanted children. However Timelord DNA is picky and doesn't want to be crossed with other species, so Susan did her best to find a way for her to become pregnant with his child. One day a Timelady came and helped."
"Who?"
"Her name was Romanadvoratrelundar she said that she had traveled with you for a time and was known by you as Romana. She took my grandparents to Gallifrey and using genetic recombinations she enabled them to conceive. My father's name was Karelos, he eventually married a full blooded Timelady and I was born some time later."
"So you were born on Gallifrey?"
"Yes."
"And Romana helped in your father's conception?"
"Yes."
"And no one saw fit to tell me what was going on in my family?" The Doctor's frustration was showing quite clearly but Sophia remained quite calm.
"Why would anyone have told you? You weren't involved with family matters anymore. From the time you were in your later four hundreds you were fairly well removed from Galifreyan society. Even in your short time leading the council, during your fifth or sixth life I believe, you remained rather distant from family matters. When Romana returned to Gallifrey it was a wonderful thing, and yet you barely acknowledged her return. You all but forgot about Arkytior on Earth and Romana was kind enough to return her home."
"I never forgot her, not for a moment. I left her on Earth so that she would learn and grow, so that she could have her own life. I may have lost touch with the family over time but that doesn't mean I don't care. I have thought about them more than ever since Gallifrey was lost."
There was a thick silence. The Doctor's anger mostly subsided but still quite unsettled by his great-great-granddaughter's presence. Sophia's cheeks had grown slightly pink with her frustration in speaking to the Doctor about family issues. Jack meanwhile remained quiet to the whole issue, since he didn't want to involve himself in family matters.
Finally the Doctor spoke, his voice much calmer than before. "How did you escape the fall of Gallifrey? And what is this warehouse?"
"Several groups felt that the Time War was reaching its climax. Those who had married non-Gallifreyians were being persecuted, and in order to be safe we scattered throughout time and space. Some used void-ships, others used chameleon arches, and people like me chose to hide among people whose DNA resembled our own. The Council tracked many of the refugees and some were killed. Later the reports came that Gallifrey was lost and the war was over. I've been in hiding ever since."
Jack picked up where she left off. "Eventually we ran into each other and both of us could tell right away we weren't quite human. So we decided to work together on a project."
The Doctor raised an eyebrow. "For Torchwood?"
Jack's smile fell, Torchwood was but a ghost to him anymore. "No, Torchwood died a long time ago, and even if parts of it still remain alive under the King's rule I haven't had anything to do with them for a very, very long time. Sophia and I stumbled across a group of people who had one thing in common: you."
The Doctor looked concerned. "Me, why was there a group about me?"
"It's not a was;" Sophia said excitedly. "There is a group about you, they're alive and well, though its founders have passed some centuries ago. Every companion you left behind, every person whose life you impacted. They started connecting with one another, reaching out, seeking other people to talk to about the incredible things that had happened while they knew you. At first Jack and I were both cautious about joining the group but when we met the people in it we knew that there was nothing but love and respect for you from those people."
"The time locked doors here," Jack continued. "Contain the archived records of the experiences each companion and friend you had on Earth until this point. Any stories they told and information they shared is stored within the computers and files we have. The records are time locked so that people can't know about the future, and each record will unlock after the event it describes takes place."
Sophia smiled. "These vaults were made in honor of you, so that one day others might learn more about you and all the good you have done. I'm glad that the records could cause you to come here as well, even if it wasn't on purpose."
The Doctor smiled; she was brilliant. Then a new idea struck him. "You said that you escaped and so did others, do you know if anyone else was outside the time lock on Gallifrey?"
She shook her head. "I would assume so, but there's no way to know for certain if any of the others survived and where they would be." She grinned a little, as if she were about to reveal a great secret. "What if we could return Gallifrey?"
The Doctor snorted. "It's impossible; don't you think that if there were another way I would have taken that course of action? The terrors Rassilon and the Daleks unleashed in the end would have destroyed everything if they had been allowed to continue."
Whatever protest Sophia was going to offer died as River announced her presence. "Well, who are our guests," she asked the Doctor.
He smiled at her, distracted from the conversation he had just been having. "River I would like you to meet Sophia and Jack. Jack, Sophia, this is River Song."
All three of them had odd expressions, none of which the Doctor could quite read. Then he saw a familiar expression on River's face, she was angry, the kind of angry he would rather be on the other side of the galaxy than face. "His name isn't Jack," she said, her voice hard and toneless.
Jack's eyes brightened, it had been far too long since someone knew he wasn't Jack Harkness. "And how do you know that," he asked, stepping cautiously towards her.
She laughed coarsely, and the Doctor was glad that she was unarmed. "You really don't remember? You tracked me down for almost two years before handing me over to the guards at Stormcage."
The Doctor looked between his wife and companion in shock; he honestly had no words for this situation.
Sophia just calmly took a seat and watched the scene play out before her. She was somewhat relieved that she was no longer the focus of the conversation.
For Jack a lot of mysteries finally made sense. He had seen River Song before, in dreams; yet whenever he awoke the dreams would fade and he would be left with just a vague impression of the memory. She was the key to the two years the Time Agency had stolen from him, and whatever he had done in that time, she didn't seem happy to see him.
"Look, I honestly don't remember you. It's been a very long time since I was a Time Agent. When I worked for the agency I did a lot of things, some of which I'm too proud of anymore. I left them when they took my memories, two years of my memories."
River's anger was more controlled, but she still clearly had an issue with him. "I'm supposed to believe that they took away every memory of you chasing me. I had only just returned to the University when you showed up trying to take me to jail." She looked over at the Doctor. "I knew that I would go to prison for killing you, but the time agency knew when and where to find me as soon as I was returned to the future."
The Doctor furrowed his brow, deep in thought. "We never talked about it, but if what you both say is true then it would seem that the Time Agency was in league with the Silence. They trained you to kill me and after they returned you to your time they sent an agent to imprison you for doing their deeds. You also never told me that you were on the run for two years before Stormcage."
"You never asked and you started showing up as soon as I was there so I didn't think about it." They stared at one another for a few moments before River changed the topic. "So you really don't remember chasing me through the sulfur pits of Langora III or the fire fight on Farris Prime?"
Jack grinned a little but shook his head. "Wish I did, it sounds like those two years were memorable for you."
River smiled. "Oh they were. So how do you know the Doctor?"
"It's a long story. We used to travel together. Why were you imprisoned for killing him?"
The Doctor and River exchanged a glance. "Long story," she said with a smirk. "You couldn't have left the agency that long ago, you don't look much older than the last time I saw you."
Jack laughed. "It's been over a thousand years since I lived that life."
"But that's impossible," River exclaimed. Then she noticed the sheepish look on the Doctor's face and the way he was shifting uncomfortably. She gave him a questioning look.
"Long story, I'll tell you about it later."
The group continued talking for awhile, getting acquainted with one another. They didn't however return to the topic that most interested Sophia, the possibility of Gallifrey's return.
Author's Note: I combined my knowledge of canon and non-canon stories for the background of Sophia. I have a goal of answering unanswered questions throughout this story, one of which was answered in this chapter: why is Jack missing two years of his life.