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In episode 10 of Full Metal Alchemist: Brotherhood, during the events in the Research Lab 5, Edward Elric is severely hurt. Later in the hospital, he writes down everything he had come to know, and he discusses with Alphonse, Hughes, and Armstrong about what to do with the information to continue the investigation.

At this point, King Bradley arrives with lemon into the room. He finds out what they are doing but acts very calm and chilled out and allows them to continue investigation while being careful.

Why did he not get Hughes and Armstrong killed at that point? Or at least tell them to not investigate at all?

  • I think he expected them to be dead or unable to stop him by the time his master plan was at the critical point. So it didn't really matter, and he chose to act cautiously and keep the farce going. – Hakase Aug 26 '17 at 0:36
  • Hughes was killed by Lust was not Armstrong. – quantum231 Aug 26 '17 at 13:28
  • I think you accidentally a word – Hakase Aug 26 '17 at 15:52
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    That's really weird question. Issue itself implies that army higher-ups are involved in this. If Bradley tell them not to investigate it, first thing they would do is to start suspect him to be involved as well. And killing? He would need to kill Edward and Alphonse as well (as Ed and Al are not persons who could just shut up about this). And 3 persons found dead in capital hospital? Giving that two of them are healthy and strong fighters. That would create a ruckus much more problematic than those trio trying to investigate this further. – lentinant Aug 30 '17 at 8:01
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    Your question implies that you have not yet wached the show in full, as this gets explained later down the line (and you're quite wrong about one thing in particular, but that's a massive spoiler). You're right to identify that some behavior (e.g. Bradley) is unexpected. But do you really want us to spoil the future story for you? I can write an answer with full justifications, but depending on the depth of the answer that will spoil most of the plot. Trust me when I say that all your current questions will be answered by the show at some point. – Flater Sep 1 '17 at 14:33
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This wouldn't work, for a number of reasons.

Ordering them not to investigate

If Bradley orders them to stop their investigation without cause, it could only mean two things:

  1. Bradley doesn't want them to discover something, implying he is somehow involved with or related to their findings at the Fifth Laboratory.
  2. Bradley is an idiot.

Since I don't think anyone present would accept the second explanation, it clearly implicates Bradley as being involved with the homunculi somehow. I doubt this would stop Mustang since he aims to become Fuhrer, and exposing the current one could help him achieve that goal. The Elric brothers would likely just be even more motivated as well.

Killing them

If Bradley killed them, it would indeed stop their investigation in its tracks, since everyone who knew about it would be dead. There might be some gossip about the Fuhrer inexplicably killing military officers, but it would probably quiet down eventually.

However,

  • He cannot kill Ed or Al since they are important sacrifices for the homunculi's plot to

    turn Amestris into a philosopher's stone.

  • He can't kill Mustang either since he's a potential candidate for the above plot.

He could kill Hughes and anyone else present, but that would just add fuel to the fire for Mustang and the Elric brothers, increasing the chances that they will discover his real motives.

For these reasons, he decided to allow them to continue their investigation in the hopes that they will be thrown off of the trail and not suspect that he is involved.

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Though this question has an accepted answer, I don't think it entirely answers the question as titled. We have covered why Bradley doesn't kill them but that's not the main question. Why did he allow them to continue their investigation? He didn't need to kill them to stop them from investigating. So why didn't he pressure them, took them captive or do similar things?

Well, the answer is: He did. He warned them about the danger these investigations pose to them, we see him dropping by several times, casually chatting with Winry, he meets Mustang with the Officers, ... Almost every time we see him, he at least implicitly threatens our protagonists. As Mustang continues his investigation, he becomes more direct and has Mustangs people transferred and Hawkeye as some kind of hostage. He even imprisons doctor Marco.

Keep in mind that we are talking about Wrath, who would like to kill every one of them just for the sake of doing so. He tempers himself at all time so it is hard for him to decide what the right amount of action/force is. He starts off with warnings and puts them under surveillance so he could have them killed when they found out too much (RIP Hughes), then he threatens them and reduces their options. He can't kill most of them so he does everything he can (except incarcerate them, but that would be super inconvenient for the plot) to make sure they wouldn't find out too much.

His only other option would have been a big bluff doubling downing on the story that he was trying to uncover the conspiracy and urging them to either work directly under him (have them under control) or to drop the investigation because it is too dangerous since it reached up to right under himself.

[Edit:] Another reason to neither kill nor incarcerate them is the fact that he still is a military leader in a time of open conflict with several neighbors. As hinted at in the series, after Scar killed quite some State Alchemists, the strength of the military is considerably weakened. Losing three more state alchemists and a living armor that would fight at Ed's side anyway does not appear to be a wise decision. Father doesn't want to waste his resources to defend the country so Bradley has to maintain the military's strength. And purposefully weakening the military at a time like this would appear odd to anyone else even if no one else could pose a thread, more people investigating would be an inconveniance.

[Edit2:] From Episode 30 on, neither Mustang nor the Elric Brothes conduct any investigation (or act against Father in any other way) that is visible to Bradley. After thier next visible steps, they become outcasts and deserters.

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