Ever since Adm. Mike Mullen blew his top over the links between Pakistani military intelligence and the Haqqani clan accused of attacking the U.S. Embassy in Kabul, there has been much speculation about what this means for America’s already-strained relationship with Pakistan.

The outgoing chairman of the Joint Chiefs of Staff went public at an appearance before the Senate Armed Services Committee last Thursday. In particular, he said that not only the attack on the embassy, but also a truck bombing on Sept. 10 that killed five Afghans and wounded 77 NATO troops, were “planned and conducted” by the Pakistan-based Haqqani network.

Mullen knows exactly what he is doing by raising the temperature with Islamabad, where anti-American sentiment is running high over drone attacks in the border areas. It comes only months after the killing of Osama bin Laden by U.S. Navy SEALs led to charges that the Pakistanis were either incompetent or complicit following the revelation that the al Qaeda leader had been living for the past five years in the town of Abbottabad.

Only 10 days ago, Mullen had a four-hour conversation with Gen. Kayani, the Pakistan army chief who used to head the ISI military intelligence, during which the U.S. official raised the issue of the ISI support for the Haqqanis. In Pakistan, there is now speculation that the U.S. will retaliate militarily for the attack on its embassy in Kabul.

The most thought-provoking article I have read since Mullen’s outburst is a piece by Bob Baer, a former CIA agent, in Time magazine. His thesis is that America has failed to understand Pakistan’s fundamental strategy in Afghanistan, and that there is no chance Islamabad will change course.

Baer says that we need to understand that Pakistan intends to bring down the Karzai government in Afghanistan (perceived as being allied with Pakistan’s archrival India), “even if that means taking on its sometime U.S. ally.”

He goes on to say that to break relations with the Haqqanis now would mean Pakistan giving up a large degree of influence in Afghanistan after the war is over. In other words, don’t expect the Pakistanis to go changing their strategy overnight and going after the Haqqanis, just because the Americans say so.