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So a different question asked if the pentagon was a legitimate military target. And an answer ended up saying, that the law of war does not apply to a terrorist organization but rather civilian law.

This made me realize this seemingly inherent paradox in waging a war against organizations which are not considered states but at the same time claiming, that the law of war only applies to states.

So can you even fight a war against a civilian organization, or do you have to recognize something as a state to fight a war against it? Are you allowed to use the military against civilian targets?

If not, how is this resolved? Is everyone just going along with a violation of international law because it would be too complex to solve? Or is this covered by something else?

EDIT (Clarification): With "you" I mean any country which might want to fight such a war on terror. Given the current situation that means primarily western countries especially the US. But if the answer is different depending on the country I would also be interested in that. And "allowed" in the sense of commonly agreed upon international law.

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    Who do you mean by "you" in the question? When you say "are you allowed..." does "you" mean "The government of the USA" and does "allowed" mean "permitted by the Geneva conventions and other Norms and Laws of War". – James K Nov 25 '17 at 22:48
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    The problem with this is that it is assuming that a number of polite fictions have some basis in reality. E.g. that "international law" has any effect if nations or other entities decide to ignore it; that there's really a "War on Terror" and not a defense against jihad; and indeed, that the recent Western idea of the nation-state is universal. – jamesqf Nov 26 '17 at 4:16
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The war on terror isn't really that much of a war in the truest sense of the word--that's just a colloquial term often connected to it. To understand what it actually is, and what legitimizes the US to go about fighting such civilian organizations, one must understand the following concept:

Universal jurisdiction allows a state to claim authority over a crime regardless of where it was committed: Such crimes are considered to have been committed against all and to be too serious to leave to the state with jurisdiction over the geographic location of the crime.

Therefore, when the US sends its troops to fight against a terrorist organization, it is not waging war against a state, but rather enforcing its law on a crime or set of crimes to which its citizens are victim and which therefore falls under its universal jurisdiction.

Postscriptum: Interestingly, however not directly relevant to this, universal jurisdiction also means that crimes committed on vessels not under the flag of any state and located in international waters can be prosecuted by any state that considers its citizens to be victims of the crime.

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    Wait, a state can prosecute a crime committed in a different country? I thought that was specifically not permitted because of the concept of self determination in international law. And if "war" is only a colloquial term and it is treated as a crime, wouldn't states have to send police instead of military? – Felix B. Nov 26 '17 at 11:33
  • Yes, states can indeed prosecute some more serious crimes committed in geographic regions that do not fall under their jurisdiction in the usual sense. See the Wikipedia article on universal jurisdiction for more information. The armed forces can in this case can be considered to be a substitute for a more traditional police force, which would be unable to eliminate the terrorist organizations because of the magnitude of their resources. The entire matter is quite similar to a war, but merely legitimized in a different way due to the fact that war can only officially be waged against states. – user18362 Nov 26 '17 at 14:47
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    Are you allowed to substitute police with military? I thought that there were laws preventing the use of military to enforce laws. – Felix B. Nov 26 '17 at 16:18
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    This is a sensible theory, but it isn't really the theory behind the AUMF of 2001 passed by Congress that justifies the existing war on terror, and declarations of war against non-state actors are almost as old as the Republic (e.g. the war against the Barbary Pirates in the 1700s). – ohwilleke Nov 27 '17 at 3:49
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    @ohwilleke can you write this as a full answer? – Felix B. Nov 27 '17 at 12:45

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