ISLAMABAD, Pakistan — The differences between the United States and Pakistan that broke into the open last week over the scale of C.I.A. operations here signaled a fundamental rift, plunging the relationship, sometimes strained, sometimes warm, to its lowest point in memory.

The rupture over Pakistan’s demands that the Americans end drone strikes — which the Obama administration rejected — and scale back their intelligence presence within Pakistan exposed the tentative nature of the alliance forged after the Sept. 11, 2001, attacks. And it is increasingly apparent that the two countries have differing, even irreconcilable, aims in Afghanistan.

With the Afghan endgame looming, suspicion is overwhelming faint cooperation between the United States and Pakistan, as each side seeks to secure its interests, increase its leverage to obtain them, and even cut out the other if need be, American and Pakistani officials say.

No one in Pakistan or in Washington now speaks of returning to the strategic alliance made by President George W. Bush and Gen. Pervez Musharraf immediately after the Sept. 11 attacks, when the primary goal was to operate joint intelligence efforts to capture operatives of Al Qaeda. Military officials from both sides say that arrangement was never bound to be a longstanding affair.