A/N: Here is the start of the next part, Days After Atlantis (I have a particular knack for titling these things). I've been posting a large volume of chapters because I really want to get it all posted, but I don't want to inundate everyone with the updates too much. Anyway, enjoy!
Part One
Emily was three weeks old when her father regenerated into his eleventh incarnation. She would never know the same Doctor that her mother had, the Doctor whose eyes she shared, or had been handed so he might cut the umbilical cord just seconds after she was born. She would know the man with a defiant belief that bowties were cool as her Doctor. He, however, would always know who her first Doctor was though.
Fortunately, when the regeneration occurred, Emily was safely accounted for with Martha, who had been ready, with arms open, to take the baby when the Doctor called her mobile. The sound of desperation in his voice had told Martha everything she needed to know. She had raced over to the park by her house, ready to take the baby and aid in the Doctor's regeneration as much as she could.
Martha had been an absolute saint, nearly becoming a mothering figure to the Doctor when he'd shown up on her doorstep nearly three weeks earlier, sobbing over the loss of Donna and toting a baby carrier with a sleeping infant. Martha had taken Emily from the Doctor and had led him into a spare bedroom, telling him to sleep and not to worry about Emily.
The Doctor slept for almost twenty-four hours before he realized that he was in a strange bed in a strange house and forgetting something rather important.
Those last few weeks had been absolutely hellish for the Doctor, who was consumed with worry and guilt, matters only exacerbated by the fact that Emily was refusing to sleep or feed from a bottle. She would eat, but only if she were very hungry, because she had quickly gotten used to Donna breastfeeding her and Emily was not ready to accommodate the situation. As for getting Emily to sleep, Martha had discovered that Emily was lulled by the sound of a dishwasher or a washing machine. It was amazing how much laundry Martha had managed to get done while the Doctor was staying at her home and how clean her kitchen was.
With all the stress and grief that was attacking the Doctor, it was no wonder that the Doctor regenerated somewhat unexpectedly. All of the emotions that were zooming through him were bound to take their toll somehow. It was rather strange, the circumstances that had spurred it on. He had been at Tesco's, getting supplies for Emily, and had slipped on a wet spot in the middle of an aisle. He'd hit his head rather forcefully and had gone unconscious. When he awoke, he could sense that something was not right, so he hurried to the TARDIS and phoned Martha, who had dropped everything to go help.
There were things a Gallifreyan child needed to learn in his or her youth, but the Doctor knew that Emily did not need to witness such things at such a young age. She was already very alert to the world, already able to process things in ways that no normal newborn could process, and would instantly find much to be upset about in her father's regeneration.
He was very glad that Emily was not in the TARDIS when it crashed. It was dangerous for him, let alone an infant. He stayed far from Martha's house for a few days, until he was certain that the regeneration process was complete, at which point he returned to collect Emily and considered filing a complaint with the clean-up crew at Tesco's.