Summary; Someone has gotten a hold of Shou Tucker's research notes. And now they want to continue what he accidentally started, which will mean a whole lot of trouble for Edward Elric.

A/N; And so we have the sequel! Welcome back to everyone who has read Truth Behind Lies and followed the story, and to everyone who has just stumbled upon this story I would very much suggest reading the prequel first, else this may not make much sense to you :) Thank you so much to everyone who reviewed in my last story and I hope you enjoy this sequel!

WARNING! This story contains major spoilers about the end of both the manga and Fullmetal Alchemist Brotherhood, as well as perhaps some of the events that occurred leading up to the end. Well… more the end of the Promised Day, but not the rest of it; this story is set perhaps a week or so after the end of the Promised Day and from there on it becomes an AU.

Chapter One;

'A partial chimera...'

It was surprising that no one else had picked up on it, and that no one had understood what a miracle (not to mention alchemic breakthrough) it was. After it had happened no one had thought any more of it, and Colonel Mustang had personally seen to it that the case was shelved permanently. After all, in their minds, nothing had actually happened so there was no point worrying about it.

'Wrong!'

They were fools, the lot of them! The military gave up their chance when they hid the evidence away from the world and told only a select few who would keep the secret even more zealously. Yet no one had suspected that one of those who had been told, while keeping the secret, would use the information for their own gain.

It was too bad Tucker had been killed not long after he had attempted to create a chimera out of the Fullmetal Alchemist. He would have been interested in his own findings, definitely.

With a sigh the man pushed away from the old, rickety desk and leaned back, staring up at the roof of the dimly lit, dank cave he was currently occupying. Across the desk was his research, the only thing he had been able to do while he was in hiding. It was best not to venture out these days; he had been seen taking Tucker's research notes back and he doubted that the fact that the government had been turned on its head in the last few days meant that the soldiers were lax.

With a frown he pulled a document toward him with the name 'Edward Elric' scrawled across the top, accidentally knocking some newspaper clippings to the ground in the process. The clippings all talked about Tucker's case, only one making mention of 'a young boy' being involved somehow.

Mustang had covered it all up, made sure that Elric's involvement was hidden so that people didn't ask weird questions. Of everyone he was probably the only one who suspected what had actually happened at that house and he took steps to protect his young subordinate. As such Elric was never mentioned be name and most of the information about him after the failed transmutation came from a second hand source who kept an eye on everything that happened in Central for him.

For example he had been told that Elric had, at some point, stopped displaying the odd, dog-like behaviour that had been the signs of the partial transmutation. Not many other people had noticed since Elric had been very careful about reigning it in, so whether the effects had actually faded with time or whether the boy had made a conscious effort to block them was unknown.

The dog, however, was still as intelligent as it had been since the incident, looking after his young mistress and protecting her from suspicious strangers. Likely this meant Elric had simply trained himself against the impulse to show odd behaviours.

The dog had probably gotten the better end of the deal at the end of the day. But he wasn't interested in the intelligent canine. No, he was far more interested in the boy that had survived the transmutation.

Which made him curse, again, the military for not looking more into the matter and therefore missing the signs that would have had them studying the transmutation and experimenting with it. Mostly everything he had figured out was theoretical and, as of yet, he had not been able to repeat the experiment without killing his 'helpers'.

He needed to get hold of Elric and examine him. Perhaps there was something in the boy's makeup now that showed how it was done and what point the transmutation needed to go to. Or maybe Elric was just supremely lucky and was one of the few that could have survived something like that.

The fact was that Elric had survived the transmutation with nothing more than a few effects. Someone had attempted to turn him into a chimera and not only was he still human but he had suffered absolutely no ill effects. How was this possible? Even the partial transmutations he had attempted so far had all ended in disaster.

Perhaps it really had simply been luck. There was no denying that Shou Tucker had most definitely been a brilliant man. His theories and experiments on chimera had been astounding and the fact that he had actually successfully created a human chimera – without letting on what it was – had once been nothing short of amazing. He had truly been an expert on chimera, and his research had been used over and over again until it had been perfected, making chimeras that looked completely human but could turn into vicious animals and had all the characteristics of those animals.

But, still, there was no way Tucker could have known what he was creating. The experiment had been interrupted by Mustang and his men... that had been near impossible to replicate because it was hard to figure out when the transmutation had been stopped. Had it been seconds, minutes?

He groaned and laid his head on the desk in front of him, frustrated beyond belief. He just seemed to keep going around in circles, never reaching the answer he sought.

He needed Elric.

Once he had Elric he would be able to work out all the holes that his research currently had. He would be able to fill information where there previously had been none, and no one would be able to get in the way of his experiments.

And once he had figured out how to do it properly? It was interesting to note that Elric's mind had merged slightly with the dog's, causing the odd behaviours in both of them. Yet Elric's intelligence had not been affected, so he had not actually given the dog anything of his. It was more that he had copied and shared what he already had. Likely the experiences and behaviours of the dog had also done the same to Elric, but that one was hard to tell since the boy was so careful about showing them.

If the animal had been conditioned to certain responses... what then? Say he had a cat who had been trained to hiss at anyone wearing green, would that response carry over? And how many times could the partial transmutation occur? The chimera transmutation could only be done once without killing the subject.

A partial transmutation, however, that was made up of subconscious thoughts and reactions and behaviours and had no affect on the physical body... it could be done far more than once. And if he could get hold of Elric he could even test that.

His hands clenched on the desk. If he could get hold of Elric. The kid was currently an Amestrian hero, he had been the only one who had been able to beat that homunculus that had been trying to take over Amestris and kill every in the country (so said his contact, at any rate, as well as the rumour mill, though most of the public only knew that he had a hand in subduing the attacking forces at Central Headquarters). He would be lucky if he could even get close to Elric, particularly since the rumours also said the younger brother was out of that suit of armour and in hospital.

So even if he did get Elric away from his guards, the older brother would probably still be hovering over Alphonse Elric. It would be a miracle to get him alone.

Who said he had to, though? He frowned in thought. He needed Elric, that much was evident, and the sooner the better. With the country in turmoil after the death of King Bradley and his son it shouldn't be that hard to slip under the radar.

For gods sake, Tucker had hidden a murder for two years, and he would have gotten away with it for a lot longer had it not been for a small, blonde brat. He, specialised in investigations and having planned this for months, could get past guards looking for enemies and maybe even take their prized hero right from beneath their noses.

Wouldn't that be a riot?

Slowly a large, predatory grin formed. A riot indeed...

FMAFMAFMA

Colonel Roy Mustang knew he had more important things to worry about then a folder that had been missing for the last few months. Generally, once he had heard about it, he would be annoyed that he hadn't found out about it until months later, furious that the culprit had not only gotten away but also had yet to be caught, and exasperated at the lax security that had allowed the folder to be stolen in the first place.

When he found out that this particular file had been stolen, however, fury was the only one of those emotions he felt. And even that was swamped by the horror and anxiety that flooded through him right after.

It didn't help that the man who had stolen it, Lieutenant Ryan Cooper, had actually been on the team that had investigated the matter to start with, so he would have originally known everything anyway. No word had yet reached the public of the cover up that had been done around the time of Tucker's death, and it didn't look like that would ever happen.

But there were other, more dangerous, issues involved in the stealing of that file. Cooper must have needed it for something, something important enough to risk going in the run for.

That did not bode well for Mustang, or Edward Elric, former Fullmetal Alchemist.

Damn it, he had to warn the kid, get him out of Central as fast as possible even if his younger brother wasn't recovered enough to go on the road. Especially with the loss of his alchemic abilities he would be a sitting duck if Cooper decided to act.

Mustang was halfway out of his chair, ready to rush to the hospital right then and there, when he stopped, frowning. Cooper had had that research for months now, and no attempt had been made on Edward so far (disregarding everything related to the homunculus, naturally). If he was going to do so the time would have been when Edward had been on the road and basically defenceless but for his younger brother.

Maybe he was reading too much into this. Breda had only told him an hour ago about the files and he was reacting instantly as though the battle situation hadn't been dispelled. Sighing Mustang rubbed his eyes; they had had a tendency to itch ever since Marcoh had helped him use the Philosopher's Stone to restore his sight.

Truthfully he was surprised Edward hadn't kicked him for that when he realised. But instead he had stared at mustang for a long time and then given a small nod and a smile, accepting Mustang's choice, and perhaps even approving it. The brothers had promised they wouldn't use the stone, but that didn't mean Mustang could not.

Slowly Mustang sat back down. He would look forward to when Hawkeye got out of hospital tomorrow, because she was his voice of reason, and she would prevent him from having any more panic attacks over small things.

With this thought in mind Mustang pushed away everything to do with the missing files and returned to the papers he was drawing up. There was nothing wrong, he was just being paranoid.

In the weeks to come Mustang would kick himself for that thought.

Next Chapter; Dealing with the loss alchemy, a recovering brother and the knowledge about his condition Edward receives news about the missing folder. Setting out to find Mustang might be a little more dangerous than he had expected, however…