When the US detained the Kuwaiti-Pakistani Khalid Sheikh Mohammed and interrogated him for years (including at least a month of harsh torture), he revealed a handful of al Qaeda operatives in the US. When Pakistan held the American contractor, Raymond Davis, and–as this NYT article specifies–had Pakistan’s intelligence service ISI interrogate him for 14 days, that appears to have led to the identification of hundreds of Americans working in Pakistan on activities not authorized by the Pakistani government.

As the article reveals, there are four things we’re doing in Pakistan to which the Pakistanis object:

1. Spying on Pakistan’s nuclear program
2. Infiltration of Lashkar-e-Taiba, the group that carried out the Mumbai bombing as well as (the WSJ adds) the Haqqani network
3. Deploying Special Forces personnel in the name of training Frontier Corps but using them to spy instead
4. Conducting the drone program unilaterally, without sharing targeting information with Pakistan

Now, we knew all of this was going on. Of course we were tracking Pakistan’s nukes; public reports often optimistically (probably over-optimistically) claim we could gain control of their program if the government was ever overturned. The Pakistanis had to know we were infiltrating Lashkar-e-Taiba, since that’s what David Headley was supposedly doing when he participated in the Mumbai bombing.

And it certainly seems like Pakistan knew the details and many of the people involved as well.

But this article provides some numbers. It explains that 335 Special Forces, contractors, and CIA officers are now being sent home. Of that, 40 to 80 are members of the Special Forces who exceeded the quota of 120 Special Forces Pakistan allowed us. The remaining 255-315 must be a combination of contractors and CIA officers whose purpose the US has not shared with the Pakistanis. That’s in addition to whatever contractors we withdrew after Davis was captured.

For the moment, it appears this will shut down two parts of the American war in Pakistan. The US threatened to shut down the training program.

The request by General Kayani to cut back the number of Special Operations forces by up to 40 percent would result in the closure of the training program begun last year at Warsak, close to Peshawar, an American official said.

The United States spent $23 million on a building at Warsak, and $30 million on equipment and training there.

Informed by American officials that the Special Operations training would end even with the partial reduction of 40 percent, General Kayani remained unmoved, the American official said.

And the Pakistanis are asking that the drone program be stopped or, at least, curtailed to its original scope.

In addition to reducing American personnel on the ground, General Kayani has also told the Obama administration that its expanded drone campaign had gotten out of control, a Pakistani official said. Given the reluctance or inability of the Pakistani military to root out Qaeda and Taliban militants from the tribal areas, American officials have turned more and more to drone strikes, drastically increasing the number of strikes last year.The drone campaign, which is immensely unpopular among the Pakistani public, had morphed into the sole preserve of the United States, the Pakistani official said, since the Americans were no longer sharing intelligence on how they were choosing their targets. The Americans had also extended the strikes to new parts of the tribal region, like the Khyber area near the city of Peshawar.

“Kayani would like the drones stopped,” said another Pakistani official who met with the military chief recently. “He believes they are used too frequently as a weapon of choice, rather than as a strategic weapon.” Short of that, General Kayani was demanding that the campaign return to its original, more limited scope and remain focused narrowly on North Waziristan, the prime militant stronghold.

Ultimately, it seems like our efforts were getting close to elements in the ISI and Pakistani military who were involved in what we deem militant activity. We were doing so without sharing our intelligence with the Pakistanis (which has often led to militants being tipped off). So now the Pakistanis are demanding we share that information again.

But negotiations don’t appear to be going well. ISI head Lt. General Ahmed Shuja Pasha left early yesterday from meetings with Leon Panetta and Mike Mullen.

Though the spokesman Marie Harf said that the cooperation between the two agencies remained on “solid footing”, the Pakistani general reportedly cut short his visit abruptly to return home.

Both the US and Pakistani officials did not give any reasons for Shuja curtailing his talks here.

There’s one more thing about this story: US reporting on it, at least, seems to pretend that Davis was captured out of chance. The NYT even repeats the implausible “mugging” story. I’d say that’s unlikely.

Update: Fixed the numbers for special forces personnel. I think.