Saddam Trial - Jurisdiction

The friend who asked, rhetorically, if the Saddam Trial was nothing but a dog-and-pony show before a kangaroo court later (but before I responded to him) asked this question:

If the invasion is illegal, the Court has no jurisdiction.

The smart money is that this is what Saddam's lawyers will try to argue. Professor Willis, my Civil Procedure instructor, concurs, but adds much more nuance. She suggests that Saddam's lawyers will specifically try to argue that the court has no jurisdiction over him because the Coalition Provisional Authority headed by Paul Bremer, under whose auspices the statute creating the Iraqi Special Tribunal was drafted, had no authority due to the illegality of the war. According to the Human Rights First page, "Iraqi Special Tribunal: Questions & Answers", the statute was actually enacted by the Iraqi Governing Council, to which the CPA temporarily ceded legislative authority for that purpose. Moreover, arguing the illegality of the war may be futile.

This is how I answered my friend:

The invasion was not, in fact, illegal, on the technical merits. Violation of ceasefire conditions + continued hostilities = grounds for war. And in the end, like it or not, war tends to throw all of our preconceived notions of law and morality out the window during its conduct.

Moreover, the jurisdiction question may be academically titillating, but factually inconsequential. Jurisdiction questions in peacetime are often subject to questions of law. However, in times of chaos (war, revolution, natural disaster), "might makes right". As I addressed in an earlier response to your initial post, no incipient government or judicial system will rule itself out of existence; and if the results are so egregious, citizens will take to revolution instead.

Here's a parallel. The First Continental Congress had no jurisdiction over the several States. Indeed, then, as now, Americans were pretty much evenly split as to handle relations with the Crown. A minority of extremists, made up primarily of lawyers, doctors, merchants, and some Southern landowners, conducted a war that was not authorized by any single State. Indeed, no State had the authority to declare war against the Crown. In fact, several Loyalists would raise the argument, and lose. While the great body of common-law continued, the questions of jurisdiction were decided in favor of governments assembled in a time of chaos (although some were "constituted" beforehand), when both the Crown and the Rebels claimed legitimacy and charged the other with illegitimacy. Thomas Jefferson made the most famous charge by laying out grievances in the Declaration of Independence. But it was neither an English nor an American court that decided in favor of the Rebels. It was the Crucible of War in which the legitimacy of independence was decided.

I understand that the legality of the war is something that many people of good faith remain hung up on. That is why I went into the second, and larger, point in my response. And I leave the larger point out there, that ultimately, "in times of chaos (war, revolution, natural disaster), 'might makes right'". I'm sure it's not a proposition that many would be comfortable with, as accustomed as we are to more-or-less peaceful progression of social history. There's also the chance that someone will want to invoke some sort of statute of limitations -- but that too is an unsatisfying answer.

The question then, dear readers, is, what is the basis for jurisdiction ab initio? In other words, how is the legitimacy of a regime established? Does the Iraqi Governing Council of 2004 count? Does the January Election count? How about the October Election? Is there even any way to determine a single act or set of acts that confers legitimacy after a "time of chaos"? If so, what is it, or what should it be?