Ali Saleh Kahlah al-Marri, alleged to be an al-Qaeda operative embedded in the U.S. to conduct terrorist attacks, will be transferred from military custody to the civilian justice system. A grand jury in Illinois is already hearing testimony, and an indictment is expected to be filed, perhaps as early as today, charging al-Marri with terrorism offenses — probably providing “material support” to a terrorist organization, among other crimes. The story is being broken by the Washington Post (here), the New York Times (here) and elsewhere (Jane Mayer had an extensive story about al-Marri recently in the New Yorker).

Al-Marri presents one of the most challenging combatant issues: the authority of the president to detain as an enemy-combatant a non-American who is lawfully present in the United States and who has been apprehended in the United States during wartime — under circumstances where the U.S. has been subjected to massive domestic attacks, and the enemy continues to threaten and attempt to attack the homeland, but where we are not currently under attack (nor were we when al-Marri was captured) and our civilian courts are open and functioning.

I’ve written about the al-Marri case here and here. There have been significant comparables: Yaser Esam Hamdi was an American citizen whom the Supreme Court ruled the president was authorized to detain without trial as an enemy combatant — but he was captured overseas allegedly fighting with the enemy. Jose Padilla, an American citizen, was, like al-Marri, apprehended in the U.S. and held as an enemy combatant — but the Bush administration evaded a Supreme Court challenge (after winning in the Court of Appeals) by transferring Padilla to civilan court (where he was convicted on terrorism charges — albeit not the ones that were the premise for holding him). And, of course, Zacharias Moussaoui, an alien who was lawfully admitted but had violated the terms of his visa by the time of his arrest, was tried and convicted for 9/11-related charges in civilian court — a circus of a case in which Moussaoui unexpectedly did the Justice Department a huge favor by pleading guilty.

The decision to try al-Marri in the civilian justice system is likely to get the administration out from under a deadline over which it has been extremely anxious. The Supreme Court had granted cert in his case, and the Justice Department was supposed to file its brief by March 23rd. That would have required the Obama administration to announce and explain its position on the authority of the a president to detain enemy combatants captured in the U.S.

By taking this action, Obama is obviously hoping to sidestep Supreme Court review — much as Bush managed to do with Padilla. There’s undeniable upside in this. I don’t think the Court would have granted cert unless the solid 4-justice liberal bloc was confident that it had Justice Kennedy’s vote to invalidate the detention. The transfer probably means the Court will now drop the case for now. Al-Marri’s lawyers will press for it to be heard anyway, but the Supreme Court will want to accommodate a new president, and nothing prevents the Court from hearing al-Marri’s claims at a later point (if he is convicted, if he sues the government, or perhaps by some other route).

But the real problem here is disclosure of intelligence — and that challenge is not being addressed much in the coverage, which is focused on al-Marri’s lengthy detention (over five years) and on what the Supreme Court may do.

Once the executive branch files charges, it loses control over discovery. There are rules in place, of course, but they are very elastic and they will be construed by a judge. The judge’s responsibility is not national security but to provide due process for the accused. We are still at war, al Qaeda is still trying to attack us, and it goes to school on the trove of information that comes out of civilian trials — both information in our files that must be disclosed and information that comes out in the courtroom during the public hearings and trial proceedings. The Justice Department’s best lawyers (who are very good) can try to draft narrow charges to minimize the potential damage, but — as Moussaoui’s case showed — they can’t control the judge (who, in Moussaoui’s case, authorized extensive discovery of intelligence gleaned from detained terrorists, at one point dismissed the indictment because she thought the government wasn’t disclosing enough, and even delved into interrogation tactics despite the fact that those tactics had no relevance to Moussaoui). It does not appear that al-Marri is a Moussaoui-like loose cannon — he is not going to save the day by pleading guilty.

The transfer decision takes the pressure off the Obama administration and probably prevents, for now, the Supreme Court from doing something reckless. But the perils it invites — perils we saw throughout the 1990s — are just getting started.