Disclaimer: I own neither Doctor Who nor Fullmetal Alchemist, just the idea for this story.
It takes place in Brotherhood, not the 2003 anime.
It had been 4 years since the Promised Day and the defeat of Father. Ed and Al had both gone their separate ways, Al to the east to research more into alkahestry, and Ed to the west to learn their Alchemy styles, having promised half his life to Winry before leaving. All was well with them, however in the heart of Amestris, trouble was brewing under the unsuspecting noses of those running the country. Raised by the current Fuhrer Grumman and Bradley's wife, Selim Bradley had been leading a secluded life, seemingly unaware of his past and powers.
But nothing so huge as his true identity could remain hidden forever, and no matter what precautions they took, no one can be shielded from their own memories. And so, bit by bit, Selim had slowly begun to remember Pride, and the power it came with. He wasn't so stupid as the reveal this, though, so in the eyes of everyone who saw him he was just the son of the previous Fuhrer who had died protecting the country who had a small ring on his forehead. But there were those who knew the truth, and knew the potential threat he posed.
Shortly after his fourth 'birthday', the killings started. Bodies dotted around the city, having their life sucked out of them. there was no external damage, but all the blood had been sucked from them, by their mouths it appeared. Sometimes in groups, sometimes just singular victims, but never any signs of a struggle, no brutality. The ordinary officers were baffled - there was no pattern to the murders, no style, no particular victims. The killer was indiscriminate and unseen.
After a 2 weeks of murders, totalling 157 across Central, the authorities decided to bring in the State Alchemists. It was decided unanimously among them that the killings were the work of alchemy, but none of them knew what sort. They daren't say human transmutation, for fear that was the case. Only one alchemist, who had been transferred from the eastern Ishvalan region for the rebuilding of their culture, had any definite clue as to what it might be.
"It looks like someone is trying to create a philosopher's stone," General Roy Mustang declared at the investigation meeting, being met with a series of gasps and suspicious glares, "It's the only possible explanation. Someone is or has created a philosopher's stone, and is using the lives of these people to strengthen it. That's why there is no discrimination between victims, and why there is no signs of a physical struggle," he explained calmly, raising his voice only slightly above the frenzied murmurs that had spread throughout the meeting.
"But why would someone want to create a philosopher's stone now? This country has made mass improvements in the past four years, and it is almost universally agreed that the State has become a much fairer, less corrupt government. Who would want to upset that?" a young State Alchemist, one who was well known to be trying to rise the ranks, piped up.
"Someone who does not like the State being fairer," Mustang said simply, and a grave silence fell among the alchemists.
"Do you really think someone is trying to overthrow the State with the creation of a philosopher's stone?" an older, much more timid alchemist asked quietly, and the heads turned to Mustang once more, eyes boring into his skull.
"I can't say for sure, the person may not even be doing this to overthrow us, but if they were, they would have to hold some particular grudge against us to go to such extremes."
In the Bradley mansion, it was a very quiet day. The guards were stationed outside as usual, and Selim was reading alone in his library. If anyone had cared to ask him what he was reading, he might have replied that it was a storybook, or perhaps a history book. He certainly wouldn't have told them that it was a book detailing the most complex alchemy, or that it held details on how to create a philosopher's stone. But no one asked him. Mainly because there was no one to ask him. His 'mother' had gone on a holiday to the south, and whilst she was free to roam the country, Selim was not permitted to leave Central.
Unbeknownst to the State, however, Mrs Bradley would never reach her destination. Two weeks ago, on the borders of Central, she had vanished, along with all her guards. No one on the train knew she was there, and it was assumed she had arrived at her home there. If anyone had cared to inspect the Bradley household, they would have notice transmutation marks hidden under a large woven rug in one of the reception rooms, along with ones on the underside of the carriage that Mrs Bradley was in.
It had been four weeks since the murders started, and although they knew that someone was trying to create a philosopher's stone, there had been no progression in who, how, or why. There had still been no sightings of the murderer, but it was noted that their range was spreading, and that they only ever took place in dark locations.
It had also been noticed that Mrs Bradley and her entire guard unit was missing. They were currently being treated as a separate case, but Selim wondered how long it would take them to put together the time of her disappearance and the start of the murders.
"Pathetic," he said to himself with disgust, "They spend so much time and effort making sure that I can't leave, that I can't find out, yet it never occurs to them that I played a child for almost 100 years. I am perfectly capable of acting, yet they buy right into my facade. Pathetic. And what's worse is that they make no attempt to restrict my knowledge of the one thing that can restore my former glory. Shelves and shelves of books, so many of them filled with alchemy, and all the lives I need. Humans really are stupid creatures."
Hearing footsteps, Selim reverted to reading his book - one with a cover of '101 Fairy Tales' - when the door opened, exposing none other than the man who he had forced into opening the gate.
"Master Bradley," Mustang said, respectfully removing his hat and bowing, "Although I know you have already been informed, your mother is currently missing. Given the circumstances, you are been taken into State custody."
"So they noticed," Pride thought to himself, "Well I wonder how many of them suspect me. The General for certain, but what proof does he have?"
Putting down his book and getting out of the chair, Selim's eyes brimmed with tears, "B-but they are going to find mummy, right? S-she is coming back?"
Mustang knelt down to see eye to eye with the small child. Having never once truly believe his complete personality switch, he was not going to be fooled by his tears. But he was smarter than to let on that he obviously suspected him, so decided to play it dumb. For now.
"We don't know when your mummy will be coming back, but for now you have to stay with us, okay?"
"O-okay," Selim said as he walked off, holding Mustang's hand for extra effect. They could lock him up all they wanted. His main work was already complete. Even if they left him under bright lighting 24/7, they couldn't capture it. He had yet to give it a name, but it's destructive power was unsurpassed. And it had the ability to spawn hundreds, thousands of copies, and go completely unnoticed, whilst he gained all of the life energy that it stole. In a few years time, others would give it a name, one that would inspire fear in all those who knew it's owner. But for now, it remained unnamed and untamed. The Vashta Nerada.
