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I'm writing a story in the genre of Heroes, The 4400 etc in which a group of apparently random civilians, mostly US citizens, are subjected to some alien influence and gain strange powers, whereupon the government wants to keep an eye on them and run tests to find out exactly what they can do.

Initially, the DHS has stepped in (they had some reason to suspect some kind of alien influence was about to show up, and were prepared for it). Would they get to keep jurisdiction, or would it be given to some other government agency?

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    $\begingroup$ So, non-alien (citizenship-wise) aliens? Maybe CDC (under Heath and Human Services). Maybe Department of Homeland Security. I could see them coordinating in such a situation. $\endgroup$ – K-C Feb 10 '17 at 1:42
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    $\begingroup$ I think that in practice, the way it shakes out bureaucratically would be very path dependent at the early stages and the precedents set in the early days or weeks of the situation and on the personalities involved, however they played out, would solidify into what in 20-20 hindsight seemed inevitable but was no such thing at the outset. The World Building forum at Stack Exchange might have more fruitful answers as I don't think that there is a true legal answer. And this might be a good question to migrate to that forum if someone knows how to do that. $\endgroup$ – ohwilleke Feb 10 '17 at 2:01
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All of them, and none of them.

Depending on your point of view, the interaction between intelligence agencies has gotten better... and worse.

Department of Homeland Security was designed to coordinate between the FBI, CIA, NSA, etc, etc on matters related to national security.

So I imagine these "alien-human hybrids" would be under the Department of Homeland Security. Throughout the monitoring, however, the exact jurisdiction of each alien will swap back and forth between departments as each department has the means to take care of a part of the monitoring.

There's a problem with this, however: each of those agencies, while nominally working with each other, are also in competition. They are their own little fiefdoms, and while they may work together most of the time, some "hybrids" will end up sucked into agencies. FBI takes one that can shapeshift. NSA takes one who can instantly see flaws in cryptograms. FAA hides a couple who can survive decompression to investigate cargo issues in uncompressed cargo planes... eventually each group will have a slice of the pie they hide from the others.

I think this inter-agency backstabbing makes for a very interesting story element; not only do the hybrids themselves have their own motives, but each government agency is playing six dimensional chess.

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    $\begingroup$ If I recall, the "etc" that Zoey mentions is a total of 17 different law enforcement / intelligence gathering agencies. $\endgroup$ – SRM Feb 10 '17 at 5:10
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just tracking them and establishing abilities likely the CDC, since they would be called in immediately when people started developing strange symptoms/abilities. Although I am sure other branches would start forming small agencies for direct use of said individuals.depending on the abilities I could see uses in nearly every department.

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    $\begingroup$ Does CDC handle anything top secret? $\endgroup$ – SRM Feb 10 '17 at 5:11
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    $\begingroup$ The CDC requires security clearances for at least some of their positions, according to CDC hiring FAQs. Not necessarily all jobs. And I'm sure they require extensive background checks for certain programs/jobs. $\endgroup$ – CaM Feb 10 '17 at 16:24
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Given the mess that the US agency org chart is today, I suspect you'd find an equally confusing mess grow out to "deal with" your powered beings.( I'm going to call them mutants for this post, though that's a terrible mis-use of the word. But it is a useful shorthand.)

Stage one: apparent chaos

At first, each department within the federal executive branch would try to cover the aspects of the "strange events" and the "mutants" that most obviously dove-tailed into their existing bailiwick. FBI would develop some teams to deal with the investigation of strange crimes. Secret Service would develop some teams specialized in both the possibility of attacks on the White House and, possibly, risks of supernatural monetary crimes. CIA and NSA would both build out teams to do deal with supernatural espionage. Each military branch would spin up at least some sort of special forces group or tactics for dealing with the threats. (So too would local SWAT teams...) And etc.

During this stage, there would also be distrust of the mutants. There would be scientific investigations. There would also be at least a beginning of recruitment efforts, to bring the "good mutants" into the folds of government to help make sense of and control the "bad mutants."

At some point, a turf war would emerge behind the scenes. A competent executive branch would most likely decide this wasn't solving problems but creating them. This would lead to...

Stage two: Federal Bureau of Supernatural

That's a branstormed title, not necessarily the best title. But the executive branch would try to consolidate the stage one spaghetti into a singular branch that was primarily responsible for monitoring, policing, and generally "dealing with" this new menace. This would draw from the various ad-hoc teams formed by the other divisions. But those other 3-letter branches of government wouldn't entirely shut down their internal teams. They'd be smaller, but not gone. So the FBI would now have fewer teams investigating these events, but they'd still have a few.

Because of that, red tape would still exist as friction between all of the branches. Just like we see today with branches that struggle to figure out who's responsible for various crimes and cases in the real world.

Especially at this stage, you'd see government actively recruiting these special people when doing so gives them an edge. The new division would include the highest ratio of mutants relative to the other, older, branches.

Military might at least toy with the idea of recruiting some kind of "team" or division or units of mutants. Though they may refuse to allow them entry at all. See their history of distrust towards people who are different from the "norm" (Women, people of color, gays, etc.).

Stage three: Hopefully they don't go there

There's a possibility of a third level stage. If the public sees these mutants as a threat, or if they do some horrible, public, thing(s), then pressure might form to suppress these new folks. If even a hint of hatred crops up in civilian populations, at least a few politicians will take advantage of it.

It is possible that entire religions -- or at least sects within religions -- will label these mutants as "demonic" or some variant thereof. This fits to historical precedent, where intolerance is not foreign to some religious sects/religious leaders.

If that hatred rises to some critical mass, then you will get some kind of effort to contain, suppress, deport, or otherwise "deal with the mutant menace." See the X-Men Days of Future Past story arc for how this might go down. Or the real-world Japanese internment camps of WW2. The higher the number of mutants you have, the more likely this becomes, at least to a point.

If this happens, then the FBS or whatever they call themselves, will militarize to a point where they feel they can take on the supers. And smart mutants will try to hide their natures, if possible. This stage may happen in place of stage 2. If the US goes this route, recruiting of mutants will be secretive and publicly disavowed. Mutants may try to seek refuge in foreign countries, to escape the hatred.

External to the US...

Depending on how many of these mutants there are, you'll see some countries welcoming mutants. And you'll see some that hate mutants, banning them and subjecting them to death sentences merely for existing. This will reflect the openness of their cultures to "outsiders" in general. Nations that generally hate differences or "otherness" will equally hate these new mutants.

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