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My overarching point was that a strong argument can be made that the GCs do not cover our conflict with al-Qaida.
GC CA2: ... the present Convention shall apply to all cases of declared war or of any other armed conflict which may arise between two or more of the High Contracting Parties ...
Al-Qaida is neither a High Contracting Party, nor do they bind themselves to the tenets of the Conventions, so the GCs do not govern our conflict with them per se.
GC CA3: In the case of armed conflict not of an international character occurring in the territory of one of the High Contracting Parties, each Party to the conflict shall be bound to apply, as a minimum, the following provisions:
Our armed conflict with al-Qaida takes place in the territory of several HPCs. However, CA3 specifically and explicitly limits its scope to only cover "armed conflict not of an international character."
There are a couple of ways to interpret this. On one hand our conflict with al-Qaida certainly crosses many international borders and, therefore, can be seen as an international conflict. On the other hand, our conflict with them is not a conflict with another nation and so the conflict could be seen as not international.
I believe the intent of CA3 was to apply some basic rules to civil wars that take place within HPCs, leaving international conflicts to the HCs and other articles of the GCs. So, I favor the first interpretation. Ultimately, it would be up to judges to determine the original intent of the Parties and either reading could easily prevail (and probably already has).
I think we can all agree that al-Qaida combatants generally do not pass the POW test, even when considering the extended Protocols. For example, the 9/11 terrorists did not carry their weapons openly before and during their military engagement with us. That only leaves potentially GCIV protections for them.
However, the first article of GCIV, after the common articles, explicitly states: Persons protected by the Convention are those who, at a given moment and in any manner whatsoever, find themselves, in case of a conflict or occupation, in the hands of a Party to the conflict or Occupying Power of which they are not nationals.
Nationals of a State which is not bound by the Convention are not protected by it. Nationals of a neutral State who find themselves in the territory of a belligerent State, and nationals of a co-belligerent State, shall not be regarded as protected persons while the State of which they are nationals has normal diplomatic representation in the State in whose hands they are.
Most of the home nations (e.g. - Saudi Arabia) of al-Qaida members are either neutral or co-belligerents with us in our conflict with al-Qaida and have normal political representation with us. So, they don't even get protection under GCIV.
Only those members of al-Qaida that are nationals of Iraq and Afghanistan that were taken captive during our conflicts in those countries would get GCIV protection, until the hostilities ended, which they have now.