"In the end, Congress placed the searches under the FISA court, but the Clinton administration did not back down from its contention that the president had the authority to act when necessary."I decided to take a quick look at FISA. My take is consistent with my earlier discussions of the Constitution. It seems to me that FISA is primarily about the gathering of foreign intelligence as a matter of routine government operation in the name of national security. Further, it seems to me that when Congress explicitly authorizes the President to use military force under the War Powers act, it is the equivalent of Congress declaring war. As such, intelligence activities at a time of war should be thought of as falling under the President's powers as Commander in Chief. I believe this is essentially what President Clinton argued, and what I understand is the position of President Bush.
But, President Clinton went farther by asserting that the Commander in Chief powers were his even if we were not involved in war. It seems the idea is that as Commander in Chief, the President has the power to act in ways that protects the national security of our country, even if the country has not committed military forces to a war against an enemy. This may well be the best definition of the President's power as Commander in Chief.
Of course we people are discussing the law and the Constitution as it has been interpreted. Much of the discussion that I've seen seems to suggest the Judicial branch of government accepts the idea that the Court has no power to constrain the President's power as Commander in Chief. So, it seems to me there are two key questions: (1) Did the President authorize secret monitoring activities as a means of carrying out the war authorized by Congress against our self-avowed enemy? (2) Does the President's Commander in Chief power embody all activities by which the President seeks to protect the national security of our nation? My own answer to the first question is yes (unless there is evidence the President used the pretense of war to spy on Americans he wanted to know about)? My answer to the second question is that at this point I tend to think it is best to include national security in general under the President's power as Commander in Chief.