I'm no fan of this Administration, but I guess I'd like to start from the right premises, rather than making odd assumptions. All in all, I think there's a bit too much paranoia here.

First, this is really just a written explanation of what would happen if there were a sufficiently awful disaster. It's hard to imagine a President (or at least one we'd want to have) who wouldn't take extraordinary, and at least arguably extralegal, measures in circumstances where there was a real loss of government continuity, like a bomb destroying the Capitol while the House and Senate were in session. (For what it's worth, taking out the Supreme Court, by itself, probably wouldn't be a sufficient disaster, since there's very little that the Court gets that really is that time-sensitive.) In other words, this is just a planning document, and probably actually just a more formal version of a memo that's been kicking around the White House since the Soviet Union got the atomic bomb. Having it out in the open actually is a little bit reassuring.

Second, in context, the "comity" language reads to me like an explicit recognition that the other branches are co-equal. The President's job under that language is to coordinate, not to run everything.

(And, by the way, I think we can assume that the courts and Congress would assert their powers if they felt trod upon, particularly the courts. They're not very shy, and generally are quite direct about claims that the executive can ignore them. For that matter, I wouldn't assume a completely pliant military, since they swear an oath to uphold the Constitution that I suspect the generals take seriously.)

That said, I do find the Administration's resistance to showing the classified appendices to the people who have oversight over those issues more than a little creepy. I am aware that it's always been the executive's view that Congress is leakier than a sieve, particularly as to really interesting stuff, but in the past that's never led to wholesale denial of access. This is, if anything, worse than the way the NSA programs were treated, and it has to make you wonder what exactly has to be hidden so well. Unless it's the launch codes for nuclear weapons (which it shouldn't be), there's no reason I can think of to deny access completely.

"In other words, this is just a planning document, and probably actually just a more formal version of a memo that's been kicking around the White House since the Soviet Union got the atomic bomb. Having it out in the open actually is a little bit reassuring."

Yes! That's exactly what it is. It continues a series of presidential directives beginning in the Cold War - most of which are either public or have public unclassified summaries. Pretty dry reading, actually. The most recent documents used in this planning document are open to the public. Presidential Decision Directive-67 (classified) and Federal Preparedness Circular-65, dated July 26 1999 (unclassified) are the main ones. Other inputs are memos from the White House (you better believe depts/agencies took them seriously, weight of law or not), formal and informal guidance from FEMA over the years. The new parts are some very very welcome new guidelines that enhance the legitimacy of government-level planning, and formally state emergency preparedness as a priority.

Conspiracy theorists will always abound, but this isn't really the right one to worry about. This is the very blue-collar side of the government, requiring the government to comply with established good business practices... which is another very welcome change in the government.

Last of all, Congress regularly checks on how the COOP programs are going. They send GAO auditors out in force, and get the results from the coordinated interagency emergency preparedness exercises.

Oh- one other thing. I don't know anything about the denial of classified annexes, so I can't comment on it. I can only comment on the vast majority of the article, which I know from in-depth experience in the field is drummed up from odd interpretations of the base document. If the article were just about the classified annexes, that would be another thing... the current article just shows ignorance of the subject matter.

Which is totally understandable as it's pretty obscure unless you work in the field.