For reasons I plan to elaborate upon in this and subsequent posts, I'm not at all convinced that the conference version of the NDAA is substantially better than the House or Senate version (or that either is better than nothing)... In this post, I'll start with the question of non-battlefield detention authority. Bobby has already flagged how the conference version of the NDAA does nothing to resolve the ambiguity concerning whether Congress has authorized the detention of citizens everywhere and non-citizens initially arrested within the territorial United States. But how that ambiguity cuts probably depends on an entirely separate question, and one on which there's been surprisingly little public debate (and on which the NDAA is itself totally silent): Must Congress provide a clear statement when it seeks to authorize such detention? That, to me, is most of the ballgame here.
To my mind, the most specific arguments for why a clear statement is necessary are statutory. Thus, Congress in the 1971 Non-Detention Act provided that "No citizen shall be imprisoned or otherwise detained by the United States except pursuant to an Act of Congress." Although Hamdi held the AUMF (which contains no such clear statement) to satisfy the NDA, that was in the hyper-specific context of individuals picked up on the battlefield in Afghanistan. The Second Circuit in Padilla specifically held that the NDA requires "clear" congressional authorization (which the AUMF didn't provide) for citizens picked up within the territorial United States. And even though the Fourth Circuit subsequently reached the opposite result in Padilla's case, its analysis turned entirely on the (disputed) claims that "Padilla associated with forces hostile to the United States in Afghanistan," and, "like Hamdi, Padilla took up arms against United States forces in that country in the same way and to the same extent as did Hamdi." In short, no decision before 9/11 or since supports the notion that the NDA can be satisfied without a clear statement for citizens who don't fit those exceptional facts, including citizens picked up outside the U.S. but not in the context of active military operations.
With regard to non-citizens, there is, of course, no Non-Detention Act. But we often forget about section 412 of the USA PATRIOT Act, which provides for the mandatory detention of non-citizens within the territorial United States who the Attorney General certifies are suspected of various terrorist activities or "engaged in any other activity that endangers the national security of the United States." Indeed, the substantive sweep of section 412 is astounding; the only reason why it hasn't been used since 9/11 is because of its procedural and temporal restraints. In her original panel opinion in al-Marri, Judge Motz explained that section 412 "establishes a specific method for the Government to detain aliens affiliated with terrorist organizations, who the Government believes have come to the United States to endanger our national security, conduct espionage and sabotage, use force and violence to overthrow the government, engage in terrorist activity, or even who are believed likely to engage in any terrorist activity." In light of such specific authorization (and the constraints on detention contained therein), Judge Motz concluded that the AUMF was insufficiently clear authority for the detention of non-citizens within the territorial United States. The en banc Fourth Circuit subsequently disagreed, albeit on exceedingly narrow grounds, and in a decision that was itself vacated by the Supreme Court.
One might also divine clear statement rules from some combination of the Fourth, Fifth, and Sixth Amendments, although my own inclination is that the statutory arguments are on firmer footing. But either way, the relevant point is that, although neither the Second Circuit's analysis in Padilla nor the Fourth Circuit panel's analysis in al-Marri are still good law, there's no law in the other direction either. And that's why the NDAA is, in my view, so dangerous on this issue; supporters of virtually every position can claim that the NDAA, by preserving the status quo, preserves their view. It might be far safer for Congress to specify what the statutes already suggest--i.e., that status quo or no status quo, it takes a clear legislative statement to hold individuals picked up in non-battlefield situations without criminal charges. But until and unless we settle the clear statement issue, this conversation is just going to keep going in circles, and anyone who thinks the NDAA resolves it one way or the other is selling something.