Pakistan has asked the CIA to all but shut down its operations in the country, demanding that the U.S. intelligence agency pull out 335 officers and contractors currently based there. Included in that number are special-forces advisers to the Pakistani security forces. Even in the worst days of the Cold War when the Soviet Union and the U.S. regularly declared each other's spies persona non grata, there was never an expulsion on this scale. And let's not forget that Pakistan is supposedly an ally.
Islamabad's immediate pretext for the expulsions was an American contractor's shooting and killing of two Pakistanis on Jan. 17, 2011. It's been reported in the press that the contractor had been working for the CIA. But other reasons cited in the country's press run the gamut, from anger over American "mercenaries" capriciously killing Pakistanis, to a suspicion that the CIA's real mission is to seize the country's nuclear weapons. And there has also been the old, lingering suspicion that the CIA somehow meddles in Pakistani politics.
The only part of the above that's true is the shooting of the two Pakistanis an unfortunate incident, which in normal times would have barely dented Pakistani-American relations. On top of it there are credible reports that the Pakistanis killed had been working for Pakistan's Inter-Services Intelligence agency, or ISI. Anyhow, the point is that Pakistan's army, which is behind the CIA expulsions, knows with absolute certainty that the CIA's sole mission in Pakistan is counterterrorism to capture or kill Osama bin Laden and the rest of al-Qaeda. If the CIA has stepped on Pakistani toes, it's been inadvertent.
The Pakistani army also ought to know that there's no way that the U.S. can put all of its eggs in the Pakistani basket. Pakistani intelligence has had no better luck finding bin Laden than the CIA has, and if Pakistan won't or can't do it, the CIA has no choice but try on its own.
The CIA's job is also to look for omens of change, especially the bad ones. When a Pakistani mob burned the American embassy in Islamabad on Nov. 20, 1979, while the Pakistani police and the army looked on, the CIA was seriously worried that Pakistan would go the way of Ayatullah Khomeini's Iran a regime enduringly hostile to the U.S. After all, unlike the mob in Tehran that seized the U.S. embassy there, the one in Islamabad intended to kill American diplomats rather than take them hostage.
Following the latest expulsions, I'd say the CIA ought to be wondering whether its old fears about Pakistan are coming closer to being realized. Remember, Pakistan receives more than $6 billion in American aid every year, and that's a lot for a poor country to put at risk by acting against its benefactor on the basis of popular suspicions that Pakistan's authorities know aren't true. Is the Pakistani army bowing to a popular rage not unlike the one that drove the mob that burned the embassy?
I'd even go further and wonder if the expulsions are not of a piece with the Arab Spring, a general rebellion against the old order. For the past 60 years, the Pakistan army has kept that popular rage at bay, stepping in when the anger has threatened Pakistan's core national security interests. Breaking with the CIA at this time suggests that the old rules may no longer hold.
Baer, a former Middle East CIA field officer, is TIME.com's intelligence columnist and the author of See No Evil and, most recently, The Devil We Know: Dealing with the New Iranian Superpower.