Notes: The long awaited sequel in my Family Timelines series is here! This will rewrite most of series six to include Rose and James. I've got huge plans through series seven at least as well, so stick around. I've left out some of the stuff in the season that wasn't vital to the main plot and I didn't see the point in changing. Huge thanks to my beta TheDoctorMulder, as usual :D
Chapter 1: Honeymoons
The Doctor, Rose, and James tried to give Amy and Rory the most amazing honeymoon they could imagine. Unfortunately, it took a few tries. First, they ended up on a space cruise that was crashing into a planet. The skies of the planet were controlled by a grumpy old Scrooge named Kazran Sardick and the little family had to convince him to be more compassionate by going back on his personal timeline and affecting his development from childhood.
In the process, he fell in love with a girl who had been locked in stasis by his father. She was terribly ill and only had a few days to live, but Rose and James convinced the Doctor to do some scans and they managed to find a way to help her live for several more years in the end. It still wasn't the forever that all couples in love would want, but it was better than a single day and they cherished every moment.
Their next attempt at giving them the perfect honeymoon, resulted in preventing an entire resort from being taken over by space pirates. They did, eventually, find a lovely beach where everyone could relax and enjoy the scenery. They even got a brief visit from a future Jamie and River (since their own version of Jamie had decided to skip the romantic sunset while on his own). Amy and Rory had decided to spend a little time off of the ship after all the honeymooning, to make sure that their friends and family were doing alright. They told the little family that they would be happy to join in for trips often, however.
James spent much of his spare time building a new vortex manipulator, since he had given his other one to River after the wedding. He also managed to convince the Doctor to start working on growing a second TARDIS for him. To their surprise, the TARDIS herself revealed that she had been growing one secretly for some time already. They were all overjoyed to find the little coral, growing happily in the nursery room that the ship had created. It would likely be a few centuries before the baby time ship was ready to fly on her own, but James knew that one day, he would have his own TARDIS and wouldn't have to rely on vortex manipulators or hitching with his parents to get around the universe.
Once his new device was ready, he decided to go pay a visit to their friends and family at Torchwood. After only a day or two, however, James received a letter in a bright blue envelope, calling him to particular time and space coordinates. So, after saying goodbye to everyone again, he programmed his manipulator for the date and time indicated and pressed the button.