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The closest well-known precedent to the 9/11 attacks I can think of is the 8 Nazi spies/saboteurs inserted by submarine during WW2. I believe they were all executed after some kind of military tribunal, but I haven't looked it up. Any opinions?
Of course, this is a wholly theoretical question because none of them survived, but I can't think of a reason to object to either the process or the result of the saboteur case being applied here.
The situation of the Gitmo detainees is entirely different. I can't comprehend any argument that says we can invade another country, capture anonymous, nonofficial, non-uniformed, complete strangers for no particular reason, and detain them indefinitely without any process whatsoever, even a military tribunal.
If we went into Somalia to capture pirates, we would have grounds to treat them as international criminals and sentence them as we wish, along with anyone who resisted us. Somali resisters (army, for example, if they had one and the government was harboring the pirates) would deserve a speedy trial to determine whether they were following orders, were defending their homes or thought they were, or were siding with the pirates out of self-interest related to crimes of piracy.
In short, GC or no GC, if criminals and pirates deserve a speedy and fair trial even if it leads to execution, relatively innocent bystanders deserve one even more, and no amount of sophistry can obscure this.