The Doctor's Secret Army
Prologue
Every time the Doctor regenerates, no matter how hard he tries, one single bit if Regeneration energy escapes into the Time Vortex. So far, a human child breathed in every strand that we know of. Vashta, his dear Silurian friend, knew that they must go somewhere, and was worried that they might fall into the wrong hands. Regeneration energy is very powerful, and a rare thing now that there was only one potential source of it left. So, she set off to find out where they went off. After years of searching and searching, she gave up and went back home. One day, though, the searched continued under very different circumstances.
On a rainy night about a month or two after Vashta returned home, Jenny heard a knock on the door. She looked outside and saw a little girl on her doorstep. Her curly ginger hair and her freckled ivory skin were soaking wet, and her big, glowing green eyes were weary. Jenny took pity on the child and gave her a place to sleep. In the morning, everyone was gone in the house (Strax was at the local pub and Vashta was out looking at cases), so Jenny made flyers and posted them around the area. When Vashta came across one, she said that she would only stay for a while. They, though, decided to do two things- keep it from Strax, who would want her to do some sort of labor that a little girl couldn't put up with, and to name her- they thought that Bliss would do, since they have never seen her unhappy.
A whole week later, Jenny got very sick. They weren't exactly sure what her illness was, but Vashta sent out to find some sort of cure. They wouldn't let Bliss in with Jenny because they were afraid that she would get sick, but Bliss missed her. After a few days, when she was sure Vashta wasn't around, she snuck out of her tiny room in the attic, and went into Jenny's room. She was lying on the bed, moaning in her sleep. She felt this urge to hold Jenny's hand, which she complied to.
Meanwhile, Vashta was back, to come and check on Jenny. When she opened the door, She saw Bliss holding Jenny's hand, her eyes glowing with regeneration energy. Her whole body was glowing, with the light moving over to Jenny. It faded soon after Jenny's body was fully glowing. Jenny's eyes began to flutter, and Bliss (who looked the same- no change to either of their appearances) let go of her hand.
Jenny had made a full recovery in under a minute.
Strax found out the next day; Vashta and Jenny were feeling guilty about not telling him anyway, so it worked out in almost every way. He found her when he was making his rounds, he decided to check in the attic for once, and found her healing herself from a paper cut she got from drawing a picture. He locked her in and waited for Vashta and Jenny to come back from lunch, and told them that he "Found a little intruder in the attic, so I put her in custody and waited to ask permission of termination". He waited to ask us because he was a guest in the house- if he wasn't then he would have terminated her in the spot. We had to explain everything to him and make him apologize to Bliss- who was very frightened when she saw "a big, scary potato man".
At the same moment, River Song had decided to intervene. She had the same idea as Vashta a long time ago, and found that the 11 known bits of regeneration energy had been breathed in by infants. She was monitoring all of them, and was startled when Bliss, whose name was actually *Joy Bloomwood, was living with them. She now intervened because everyone in the house knew. Her theory is that every kid will get a certain power from the regeneration strand, power that can be used for good or bad. They all agreed that River would look for the children with the Vortex Manipulator and report back every few months so we could see her progress, and we would house the children, raise them, and eventually train them so that they can be the Doctor's secret army- to fight with and for him when he needs them the most. The only thing is that the Doctor must never know.
*They will keep calling her Bliss, they had already gotten used to calling her that, and they thought it suited her more.