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 Pakistans 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, a report in the New York Times said on Monday. 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. There was never a level of trust, said a former American military official who served in a senior position in Pakistan. Im convinced now they dont want our help. The American official did not want to be identified while discussing the delicate nature of a relationship that, whatever its failings, both nations are reluctant to jettison completely. But politicians on both sides are disappointed with the results of billions of dollars in American military and civilian assistance since 2001, and the Obama administration acknowledged to Congress in a report this month that the results of the spending fell short of expectations. In any case, the money has done little to pave over the accumulating strategic differences between the two nations. Broadly, the Americans seek a strong and relatively centralized Afghan government commanding a large army that can control its territory. Almost all those ends are objectionable to Pakistan, which while it calls for a stable Afghanistan, prefers a more loosely governed neighbor where it can influence events, if need be, through Taliban proxies, the newspaper said. The particular differences revolve around which Taliban factions should be included in any settlement; the role of India, an ally of the United States but the enemy of Pakistan; and the size of the new Afghan Army, which the Americans want big and the Pakistanis want small. The situation is further complicated, American and Pakistani officials said, by discord within the Obama administration over how the United States should withdraw troops from Afghanistan, and what role, if any, Pakistan should play in the exit. The overall commander in Afghanistan, Gen. David H. Petraeus, is determined to batter the Taliban as much as possible, a policy that the Pakistanis disagree with, both sides say. Pakistan prefers that the State Department tilt toward reconciliation between the Afghan government and the Taliban. Even within the Pentagon, the chairman of the Joint Chiefs of Staff, Adm. Mike Mullen, who has met with the Pakistani military chief, Gen. Afshaq Parvez Kayani, on more than two dozen occasions, has more tolerance for the Pakistani point of view than does General Petraeus, a senior American official said. With his position in Washington, Admiral Mullen could still prevail on persevering with Pakistan. These American nuances are well known at the Pakistani Army headquarters in Rawalpindi, where General Petraeus is referred to as Mr. Petraeus a calculated omission of his military title as a way to mock his perceived political ambitions, according to a recent visitor to the headquarters. For months, Pakistans diplomats and military officials have complained that they were being kept in the dark by the Obama administrations maneuvering, no matter how preliminary, for a negotiated solution in Afghanistan. There is no transparency; they are not telling us who they are talking to, a Pakistani government official said. Another official, in Pakistans security apparatus, said: We dont know what the Americans endgame is in Afghanistan. As their nervousness about American intentions have increased in recent months, the Pakistanis have sought to improve their leverage threatening C.I.A. operations in Pakistan, cracking down on Taliban leaders to coerce their cooperation, and trying to befriend President Hamid Karzai of Afghanistan, who has also felt on the outs with Washington. In the latest iteration of this new Pakistani-Afghan relationship, General Kayani and the head of Pakistans intelligence agency, Lt. Gen. Ahmed Shuja Pasha, accompanied Prime Minister Yusuf Raza Gilani on a visit to Kabul on Saturday, the most public of a number of visits to Afghanistan by General Kayani in the past year. American diplomats in Islamabad and Kabul declined to comment on the Pakistani visit to Afghanistan, and appeared to know little about the intention of the Afghanistan-Pakistan Joint Commission unveiled with considerable fanfare by the two sides in Kabul as a vehicle to end the war. To some extent, the Americans have been coaxing the Afghan and Pakistani leadership to talk to each other, but not at the cost of keeping the United States out of the loop, or of concocting solutions that are against American interests, American officials said. The Pakistanisefforts to improve relations with Mr. Karzai, whom until recently they had given the cold shoulder, was but the latest example of attempts to sidestep the United States in order to safeguard Pakistani interests in Afghanistan. In a nod to General Kayani, Secretary of State Hillary Rodham Clinton met the general on the sidelines of a conference in Munich in February and pledged that Pakistan would be included in the negotiations, a Pakistani and an American official said. But distrust is carrying the day, as the dispute over the drone campaign showed. For some time, in fact, Pakistani security officials say, the Americans have refused to share information on their targets and have gathered intelligence on them on their own, using their own network of agents and informants. The senior American official in Washington acknowledged that in many instances the Pakistanis had been cut out because they were not trusted. In the past, targets had escaped from the drones after word of the attack was leaked. That would presumably be by the Pakistani side, which still favors a strategy of choosing between good Taliban, those who do Pakistans bidding in Afghanistan, and bad, those who do not. The feeling of being allies was never there, a senior Pakistani military officer, who has interacted closely with Washington since 2001, said. Ive said to the Americans: 'You are going to fail in Afghanistan and you are going to make us the fall guy. I still think this is going to happen.