A U.S. operation in the mountains near Afghanistan last November killed 24 Pakistani soldiers. Pakistan wanted an apology. The U.S. refused. In response, Pakistan shut down supply routes to Afghanistan for NATO convoys.
After intense talks, two border crossings were reopened last week to convoys for the U.S. and NATO forces.
Pakistan's ambassador in Washington, Sherry Rehman, was at the center of the negotiations. Afterward she called it a moment of great opportunity for the two countries.
"Now that it's resolved to both sides' satisfaction, I would think that we could use this time and space to build on convergences," she said. "There are many differences that we have been able to narrow in the last few months."
Secretary of State Hillary Clinton, who was also involved in the negotiations, was more candid about the "hard questions," as she put it, that remain between the U.S. and Pakistan. "I said many times that this is a challenging but essential relationship," she said. "It remains so, and I have ... no reason to believe that it will not continue to raise hard questions for us both."
Analysts in Pakistan have their doubts that things between Pakistan and the U.S. will now turn rosy.
"Is it going to open up avenues for improvement, greater improvement in relations?" Ayesha Siddiqa said. "I'm a bit skeptical."
There are several hard questions that have been impossible to resolve.
One is the U.S. drone attacks against militants inside Pakistan. The Pakistani government says it wants them to stop, although it is widely believed that the government really wants access to the intelligence the CIA uses to choose targets.
Pakistanis of all stripes hate the drone attacks, retired Lt. Gen. Saleem Haider said.
"You can't undertake unilateral attacks on Pakistan's soil and say that you are friends of Pakistan and you will be a non-NATO ally," he said. "There's a contradiction in this."
Even more difficult is the issue of the Haqqani network, a pro-Taliban, pro-al-Qaida insurgent group that finds sanctuary in northwest Pakistan and crosses the border freely to attack U.S. and NATO forces.
The U.S. believes the group is essentially a subsidiary of Pakistani intelligence.
This problem cannot be resolved to the satisfaction of the U.S., Siddiqa said. "Here is an issue of strategic divergence," she said. "The Pakistani government does not want to pursue and kill Haqqani and his network — simple as that."
In Pakistan these divergences with the U.S. are deeply felt, and they've given rise to intense anti-Americanism, evident at a protest of thousands this week and a march from Lahore to Islamabad. In Lahore a few days ago, many slogans and banners called for closing the border to NATO resupply convoys once again and for jihad against the U.S.
There is also deep suspicion here that Pakistan's government is colluding with the Americans. Pakistanis believe there is public posturing while something else goes on in private.
"Most Pakistanis are clear that the Americans do what they do in and around this country, not in spite of the Pakistani leadership, but with the consent of the Pakistani leadership," said Aasim Sajjad, a professor of history at Quaid-i-Azam University in Islamabad.
Sajjad said he believes that under these circumstances, the U.S. will always have the upper hand.
One senior American official says this is a "relationship that really matters," and that military and intelligence cooperation need real improvement.
Whether the two sides are capable of pulling that off is another of those hard questions.