I WORKED on Pakistan policy in the US government from October 2007 to July 2011. Within that timeframe Pakistan closed Nato routes twice in response to cross-border strikes that resulted in the deaths of Pakistani soldiers.

Each time the routes closed, I recall US policymakers waiting with bated breath for them to open again. In those days the dependency on Pakistan for the transport of Nato supplies, especially fuel, was much higher than it stands today.

I also observed many senior US officials taking great pains to point out to Pakistan’s critics that the majority of Nato fuel made it to Afghanistan only with Pakistan’s cooperation. US officials were not publicly accusing Pakistan of complicity with militants in the war in Afghanistan. Congress was preparing to develop a long-term aid commitment known informally as the Kerry-Lugar-Berman bill. The US was advocating on Pakistan’s behalf with other bilateral and multilateral donors as well as international financial institutions. The routes would open up within a month’s time.

Those days are long gone. From my new perch outside government, I watched the latest route closure drag on for over six months. Both sides boasted about how they no longer needed one another, implying that waiting until the other side blinked would not hurt them. The US revealed it could depend entirely on the Northern Distribution Network through Central Asia — a deliberate effort on the part of the Obama administration to reduce dependency on Pakistan. Pakistan said it could live without American money even though its vulnerable foreign-exchange reserves indicated otherwise.

The prolonged time frame was not for nothing — 24 Pakistanis were left dead after the November incident at Salala. Even with this tragedy, I still expected the two countries to wrap up their latest tiff much quicker than they did for no other reason but the fact that both need each other when it comes to Afghanistan policy.

I was wrong. Afghanistan is what continues to drive both countries further apart. When the US did not formally apologise for the 24 deaths, it became harder for Pakistan’s military to sell cooperation with the US to its rank and file. For the US, apologising became a problem in itself, as many in the Washington policy community were alleging Pakistani state support for Haqqani-network attacks against the US in Afghanistan.

But the challenges go beyond just Afghanistan. As both governments attempted to iron out deep-seated problems in their relationship, they were forced to contend with other political realities, such as national elections, weak economies and staunch opposition voices in both countries. Ironically, Barack Obama and Asif Ali Zardari — two presidents who couldn’t be more different — found themselves in very similar political situations.

It should come as no surprise that the American and Pakistani media, politicians and civil society have a lot to stay — mostly negative — about US-Pakistan relations. For two countries that have grown accustomed to playing cloak-and-dagger politics with (and sometimes against) one another, this is an unwelcome set of circumstances.

But perhaps this is the only way. For the relationship to mature and evolve into a partnership among equals, both sides of the aisle in both countries must critique, question, poke and prod the parameters of US-Pakistan ties. Pakistan’s parliament intended to do just that in April when it developed a 14-point agenda for relations with the US. American congressional efforts to condition aid to Pakistan occur in the same vein.

But these approaches only scratch the surface of what needs to be done. The parliamentary review is not legally binding and the conditions Congress places on assistance to Pakistan often result in more bureaucratic work for US agencies rather than substantive changes in policy.

I, for one, still have many questions about the negotiations on Nato supply routes. I know others in Washington who follow the relationship are asking the same: how did the US come to finally apologise when it was so adamantly opposed to the idea? Did Pakistan receive more financial assistance beyond the delayed Coalition Support Funds? Did it push for a greater role in US negotiations with the Taliban? Did the US finally convince Pakistan to go after the Haqqani network? Will Pakistan close the routes again? Is Pakistan’s parliamentary review no longer relevant?

The two countries say they are close to finalising a memorandum of understanding on the supply routes. And in my many conversations with American and Pakistani policymakers in recent weeks, it is apparent that both sides share at least one thing in common: a genuine interest in getting back on track. I don’t expect the MoU to answer all of our difficult questions, nor is it likely to be a legally binding document. As Secretary of State Hillary Clinton said of the relationship, “I have no reason to believe that it will not continue to raise hard questions for us both. But it is something that is in the interests of the United States as well as the interests of Pakistan”.

In this spirit, I do hope the resolution of the Salala incident and the MoU provide an opportunity to reset the tenor and attitudes of both countries when it comes to cooperation. It would behove each to stop asking the other if it is a partner or a adversary. We’ve heard enough talk like this, especially after a six-month standstill in relations, 24 Pakistanis dead and millions of dollars lost. It is simply too costly to go back to where we came from.

The writer is an analyst at the Eurasia Group and a senior fellow at the New America Foundation. She served as director for Pakistan and Afghanistan on the White House National Security Council from 2010 to 2011.