Benjamin Wittes at the Lawfare Blog has written a terrific explainer on what the NDAA does, and does not do.

Key point rebutting the contention that the indefinite detention provisions apply to United States citizens:

Section 1022 purports not merely to authorize but to require military custody for a subset of those who are subject to detention under Section 1021. In particular, it requires that the military hold “a covered person” pending disposition under the law of war if that person is “a member of, or part of, al-Qaeda or an associated force that acts in coordination with or pursuant to the direction of al-Qaeda” and is participating in an attack against the United States or its coalition partners. The president is allowed to waive this requirement for national security reasons. The provision exempts U.S. citizens entirely, and it applies to lawful permanent resident aliens for conduct within the United States to whatever extent the Constitution permits. It requires the administration to promulgate procedures to make sure its requirements do not interfere with basic law enforcement functions in counterterrorism cases. And it insists that “Nothing in this section shall be construed to affect the existing criminal enforcement and national security authorities of the Federal Bureau of Investigation or any other domestic law enforcement agency with regard to a covered person, regardless whether such covered person is held in military custody.”

And this point regarding Guantanamo Bay facilities:

Sections 1026 and 1027 prevent the use of federal funds for building detention facilities in the United States or transferring Guantanamo detainees to domestic facilities or releasing them into the United States. It effectively continues a congressional policy of preventing more Article III criminal trials of Guantanamo detainees and preventing the construction of alternative facilities that would enable President Obama to fulfill his promise to shutter Guantanamo.

I have argued for a very long time that Congress, not the President, was responsible for the failure to close Guantanamo, mostly to deaf ears. This bill passed with a huge bipartisan majority in both houses, so I'm unsure how anyone but Congress can own this now.

Wittes has more on that later in the post:

Yes. The NDAA does three things that make it impossible, at least during fiscal year 2012, for President Obama to fulfill his promise to close the detention facility at Guantanamo Bay. It forbids him to spend any money readying an alternative site to house detainees in the United States. It forbids transfers of detainees to the United States. And it makes it difficult–though a little less difficult than it is under the current spending restrictions–to transfer detainees to third countries. To close Guantanamo, the administration would have to transfer a bunch of detainees to other countries, and it would have to move a bunch of other detainees to some alternative facility. So as long as these restrictions exist in U.S. law, Guantanamo is going nowhere. These restrictions, it is worth noting, are already in current law. So while they are (in our opinion) bad ideas, they are by no means new the NDAA.

Finally, there is this bit which should actually please civil libertarians. It was added as part of the negotiation after the President's veto threat:

Section 1024 of the bill, as we’ve noted, requires that people subject to long-term military detention in circumstances not already subject to habeas corpus review–think the Detention Facility in Parwan, Afghanistan–henceforth shall have the right to a military lawyer and a proceeding before a military judge in order to contest the government’s factual basis for believing them to be subject to detention. This is an extraordinary and novel development. Detainees in Afghanistan currently have access to the Detainee Review Board process, which as described in this article already provide a relatively robust screening mechanism, particularly compared to years past. The DRB process does not include lawyers and judges, however, and human rights advocacy groups have criticized them on this ground. Requiring lawyers and judges to staff out the screening process is a pretty remarkable shift in the direction of accomodating those concerns.

This is the most cogent explanation of the counterterrorism provisions in the NDAA (which covers far, far more than this) I've seen.

As far as the politics go, when both houses of Congress have passed it with a veto-proof majority, I doubt there will be a veto forthcoming. The President could sign it and add a signing statement to the more troubling provisions. While this would certainly get some criticism from the right wing given his criticism of President Bush's use of signing statements, a signing statement would offer some clarity and political cover for signing a bill that had no hope of having a veto sustained. But whether or not he decides to go that route, it's worth reading and bookmarking Witte's post for reference, because the misinformation is flying around the Internet in a swarm right now. Ron Paul supporters, in particular, seem to be spreading mountains of misinformation. But that's a story for another post.