The internal debate within the Administration over when and how to draw down in Afghanistan, and with how many troops, has begun. As I understand it, General David Petraeus will offer a range of options, and the national security team will assess them, with Obama having the final decision. As the LA Times notes, both Bob Gates and Petraeus, the ones most associated with a smaller drawdown, are leaving their posts, while those pressing for a scaled-back presence like Joe Biden remain in power. So it’ll be interesting to see what comes of this, though you can’t go wrong betting on a middle course, nothing dramatic.

But the more consequential secret deliberations over the future of Afghanistan are taking place in Kabul. As I noted last week, the US really wants permanent bases in Afghanistan, from which they can launch attacks and covert operations against terrorist groups, like they did against Osama bin Laden. These talks are happening right now, and it’s even less clear where they’re heading:

American and Afghan officials are locked in increasingly acrimonious secret talks about a long-term security agreement which is likely to see US troops, spies and air power based in the troubled country for decades.

Though not publicized, negotiations have been under way for more than a month to secure a strategic partnership agreement which would include an American presence beyond the end of 2014 – the agreed date for all 130,000 combat troops to leave — despite continuing public debate in Washington and among other members of the 49-nation coalition fighting in Afghanistan about the speed of the withdrawal.

American officials admit that although Hillary Clinton, the US secretary of state, recently said Washington did not want any “permanent” bases in Afghanistan, her phrasing allows a variety of possible arrangements.

“There are US troops in various countries for some considerable lengths of time which are not there permanently,” a US official told the Guardian.

It’s pretty clear what the US wants: a staging ground for future operations. The bases discussed here would harbor “large contingents of American special forces, intelligence operatives, surveillance equipment and military hardware,” according to The Guardian. They are seen as “strategic assets” in an inhospitable part of the world.

Military operations are increasingly going underground, with the military and intelligence apparatus merging (see Petraeus’ move to CIA, and CIA Director Leon Panetta’s shift to run the Pentagon). Panetta made no bones about desiring more secret wars and covert operations in his confirmation hearings to run DoD. That requires regional bases where these covert ops can launch from, and Afghanistan is perfectly situated.

With these covert ops, you don’t have to rely on coalition partners like NATO, who Gates harshly criticized as practically irrelevant last week. You don’t have to go through that messy business of capturing detainees and prisoners of war, only to find that most of them are civilians – a drone strike or an assassination directive handles that unfortunate business nicely. And you don’t have to engage in that awful nation-building, where you turn countries into unsustainable police states.

It’s just perfect, except for the inconvenient reality that it’s completely illegal under US and international law.

Afghans rejected the first stab at a strategic partnership agreement, and regional powers like Russia, Pakistan, China and India have made their concerns over a permanent US presence very clear. In particular, Afghans do not want US bases to be used to launch an attack outside the country, which seems to be the entire US goal. So this has a ways to go; Iraq successfully fought against permanent bases in its country and got a status of forces agreement for military withdrawal.

I do think, however, we can say with some degree of certainty what the US wants.

UPDATE: On a related note, here’s Jeff Merkley on why we have to bring the troops home now.