In the TARDIS kitchen Amy, Rory, and Martha were sitting at the table drinking something that looked like soda that they had found in one of the cooling units. They were all exhausted but decided to unwind a little before going to sleep.
"I can't believe how different the TARDIS looks," Martha was saying.
"What was it like when you traveled with him," Rory asked.
Martha smiled, remembering it fondly. "It looked like coral or something. It felt much more organic. Now it feels so futuristic."
Amy sat up a bit. "We saw the coral control room one time. Apparently she stores the data somewhere in her matrix. Which one do you like more?"
"This one actually. I mean the other one was my home and will always feel like home, but this one is... well cooler."
The others nodded. "I wonder what they've decided to name our grandchildren," Rory pondered.
"Something better than 'Doctor' I hope," Amy replied with a grin.
Then they heard a familiar voice from the hall. "The happy couple is resting so that must mean the voices I hear are her parents." Through the doorway stepped Jack Harkness with a smile on his face, which quickly faded into shock when his eyes fell upon Martha. He shook it off quickly and then proceeded to pick up the tiny woman in a firm embrace. "Martha, I've missed you."
She eyed him carefully. "I saw you just the other week and you didn't look so... old..."
"Different Jack," Rory answered carefully.
"Same me, different time," Jack added. "I haven't seen you in... centuries."
She laughed in shock. "Sometimes I forget that you can live forever."
"The last time I saw you..."
She cut him off, seeing the sadness in his eyes. "I'm assuming it was my funeral and I'd rather not think about that."
"Alright then, let's have a glass of whatever this is to toast the birth of the twins!"
The idea was readily agreed with and the four time-travelers toasted the occasion with the soda-like drink they had found. It wasn't too much later that they all laid down to sleep, exhausted from the long day.
With many hugs and a few tears Martha and the Williams family left the TARDIS the next day. River stayed with the Doctor with the promise that she would visit regularly.
The birth of the twins affected quite a change in the Doctor. Instead of flirting with one new danger after another he found himself being rather cautious and worried. While he wasn't obsessive about the safety of the children he had a new found tendency to avoid anything that looked remotely dangerous as a destination. They took to traveling between Haven and the Williams home at varying intervals.
However Jack Harkness found himself quite at a loss for what to do anymore. He was a man with no home, no place in time, and no purpose. He had spent so many centuries at the time vault with Sophia that now, with her missions complete he had no more to accomplish. So he took to spending time in the storage areas of the TARDIS, exploring everything that had been left behind throughout the centuries.
He was in the midst of a pile of odds and ends that included a Union Jack t-shirt when River came down and sat next to him.
"I swear some days you look just about as lost as I feel."
He held the shirt a moment, lost in a memory, before looking at her. "I've lived so long, and some days I feel the weight of it all. I keep thinking I'll find a new purpose but I'm not sure where to find one." He folded the shirt carefully and placed it back on top of one of the piles.
"I was raised to be the Doctor's murderer; sometimes it's better not to have a purpose."
"You found another purpose in life though."
"Did I? I fell in love with the Doctor, made him my life. Either way, for good or for bad he has been the entire focus of my life. Yes I love him, and I love our children and our life, but there are days when I would give anything to live the life of my younger sisters and brother."
"To be normal again?"
She laughed. "To be normal at all in my case. You'll find your purpose again Alexander."
It was his time to laugh. "Ahh my old alias, Alexander Kledak. And here is something of mine from around that same time." Not too far from the Union Jack shirt was a sonic blaster which he picked up and handled gently. "The Doctor changed me. I was angry with the Time Agency for taking away my memories, which apparently has everything to do with you. I became a con-artist, found the name Jack Harkness and then met the Doctor. That was millennia ago for me, centuries for the Doctor, and I can't even begin to guess how long for you."
"Since I was convicted of killing the Doctor it's been about thirty years. I'm able to slow and reverse how my physical age appears, but I won't live forever."
He nodded. "Then make the best of it. I think I know where to go. Here take this, it got me out of a few scrapes when I used it, hopefully you can get some use out of it too." He handed the sonic-blaster to River and she accepted it with thanks.
"Where do you want to go?"
"I've already seen the end of the universe; why not watch it from the beginning?" He gave her a beautiful smile which she returned with a similar one.
Very shortly thereafter Jack Harkness, the man whose true name was lost to time traveled to one of the oldest galaxies in the universe to see time from very near to the beginning. Many eons later he would meet the Doctor again. At that point he was a very different creature, a wise and ancient being who had seen the beginning and the end who had a simple message to bring the Doctor, that he was not alone. The Doctor however had already seen the end of that tale.
Rory and Amy meanwhile were enjoying raising their three younger children. Hope, though she had shown no signs of being changed in the same ways River had, began to do high level mathematics while she was still too young to be in school. While this worried her parents, River suggested that they just explain it away as her being gifted and not to worry so much about the children.
The Williams family also became two of the founding members of a small society of individuals who knew or had traveled with the Doctor. It wasn't long before a much younger Jack Harkness arrived, followed quite closely by Sophia. The group shared their memories of the Doctor and their travels with him. Sophia and Jack proceeded to record the stories of the companions and saved them for the future generations of companions.
Amy and Rory, Martha and Mickey, as well as Sarah Jane never shared with anyone the secret of River Song and the Doctor, that secret was far too important to keep. Rumors of River Song did make it into the archives, some saying she married the Doctor while others proclaimed her his murderer. These archives were the very same ones she came to study when she researched the Doctor to become a Doctor of Archaeology.
Callum and Olivia grew up from the perspective of their family at about the same time that their aunts and uncle were growing up, though their intellectual capacity was much greater than that of their non-Timelord kindred. They loved their human family and the time the spent on Earth with their very young grandparents. Upon reaching adulthood however, they decided to go to Haven and help complete the work of the refugee Timelords.
Not long into their settlement on Haven the Doctor reached a very old age, and for only the second time in his eleven long lives the Doctor regenerated due to age. The new twelfth Doctor was still quite energetic, but much less clumsy than his eleventh incarnation. He was wise and mature, and still very much a wanderer.
"Well River what will we do now? Our children have grown up and there is still whole universe to explore."
She laughed. "New body new desire to travel again? Oh my love, I had worried that you wouldn't want me around anymore."
He looked at her solemnly. "I will always want you around River, always. My feelings for you haven't changed."
"I'm glad. I think that right now what I want to do is return to the time I lived the longest in. I want to teach archaeology. And you can finally travel the universe again, our children are grown and have chosen to remain on Haven, but this isn't my home."
He looked at her sadly and nodded. "I understand. I can take you there of course..."
She kissed him, noting in her mind how different and yet similar he tasted. "You had better visit and come whenever I call."
He laughed and grinned, she was still his River and he was still her Doctor. "It's a promise."
So he returned River Song to Luna University where she became one of the most respected professors of archaeology. She also developed a reputation as a freelancer in many fields. The Doctor visited her frequently and whenever she called. Callum and Olivia would also visit and bring her updates on how the project was progressing.
Haven's inhabitants had grown over time, and their ability to access Gallifrey was almost complete. They constructed two towers which would act as a gateway into the space between all universes and dimensions. It would only be a matter of complex calculations and experimentations before Gallifrey was freed of the terrors and safe to travel to from many universes. The Timelords of Haven also came to call their world by a new name. Haven became Darillium.
Not that many chapters left, just having difficulties that make it hard to write. Reviews appreciated.