The immediate question is who bears responsibility for a strike in which 22 civilians, including doctors and patients, were killed in what the Nobel prize-winning NGO branded a war crime. But the disaster also raises a list of troublesome tactical questions for Washington.
Those questions could not come at a worse time for President Barack Obama, who is facing a much wider strategic dilemma over a war that as a candidate he termed "the right battlefield" for America but that has haunted his entire presidency.
Heading into his final year in office, Obama is weighing whether to go ahead with his plan to bring home almost all U.S. troops in Afghanistan next year to honor a political promise to end the wars he inherited. He may instead opt to leave behind a reduced, but still considerable, U.S. force to boost the country's vulnerable military forces amid fears that they could eventually collapse under Taliban pressure.
A debate on U.S. tactics
Even before all details of the attack are established and Obama delivers his recommendation on troop numbers, the tragedy is provoking debate on the dangers inherent in the arms-length U.S. tactics in Afghanistan where American forces are supporting Afghan units who lack their own air support but not leading the fight themselves.
"The Afghan proxies on the ground have always been unreliable. Our forces are so thin in Afghanistan, we don't have enough people there to fight a war," former CIA officer and CNN intelligence analyst Robert Baer said. "We simply can't carry out air attacks based on Afghan reporting."
In a broader sense, the plight of Kunduz, and the fact that it fell to the Taliban
at all, casts an unflattering light on Afghan forces built with billions of dollars from the U.S. and its allies in a bid to provide a rational for foreign troops to go home.
"The fact that the Taliban were able to gain control of Kunduz was a strategic surprise," said Nora Bensahel, an expert on U.S. defense policy at American University. "It does call into question some of the capabilities of the Afghan security forces."
Kunduz is not the only area in which the Taliban has lashed out at Afghan forces during this summer's fighting season, which has seen thousands of Afghan National Army troops die, a rate U.S. military officials warn may be unsustainable.
The Army has clashed with the militia across northeastern Afghanistan and struggled to contain a string of attacks in Kabul itself, including a car bombing of an Afghan member of parliament Monday. Large areas of the country outside the major cities remain beyond the control of government security forces. In some areas, the Taliban holds the land -- in others warlords operate fiefdoms where there is no dominant security player.
It is against this worrying backdrop that Obama must consider whether to go ahead with his already stated plan to leave only around 1,000 U.S. troops in Afghanistan -- mostly to protect the U.S. Embassy -- when he leaves office in 2017, down from around 34,000 American soldiers in the country when he became president in 2009.
Since then, he has tried multiple strategies, all with limited success: He has surged troops into the war, established withdrawal timelines, pulled thousands of U.S. troops home and struggled through years of antagonism with former Afghan President Hamid Karzai.
Through all that, his vow to get American troops home from Afghanistan -- to match his withdrawal from Iraq -- has remained crucial to the President's political legacy.
Obama has tried to end a war that killed more than 2,300 U.S. soldiers. At the same time, he has wanted to create the conditions for a responsible departure that would leave the Afghan government capable of defending itself and prevent Afghanistan lapsing into the kind of terrorist haven that a Taliban government provided to Al-Qaeda while it plotted the September 11 attacks. It has been a difficult balance to strike.
Slowing the pace of withdrawal
The recent upsurge in violence in Afghanistan and the difficulties the administration has had extricating the United States from a war that started 14 years ago has left some in Washington unsure over the end game in the conflict.
The war has yet to filter much into the 2016 election campaign, but in one statement Tuesday, Republican front-runner Donald Trump stoked controversy by saying on Fox News that the U.S.-led invasion of Afghanistan was a "terrible mistake." He added, however, that U.S. troops needed to stay to avoid a collapse of the government.
Trump's comments put him at odds with mainstream opinion. Whlie there have been frequent criticisms of the manner in which the George W. Bush and Obama administrations have fought the Afghan war, there has long been a political consensus in Washington that it was the correct decision to target al Qaeda and its Taliban hosts in Afghanistan.
Obama has already slowed the pace of plans to cut the current 9,800-strong U.S. force in Afghanistan to 5,500 by the end of the year.
And The Washington Post reported on Monday that a decision on the post-2016 U.S. troop presence could come soon, with Obama was seriously considering keeping 5,000 U.S. troops in Afghanistan after he leaves office -- five times the size of the garrison he had originally planned to keep in the country.
The top U.S. commander in Afghanistan, Gen. John Campbell, said Tuesday that assumptions had changed on the strategic needs for troop levels in Afghanistan based on an uptick in insurgent activity, an increased Al-Qaeda presence and signs ISIS might also be targeting the country.
"Based on conditions on the ground, I do believe we have to provide our senior leadership options different than the current plan we are going with," Campbell told the Senate Armed Services Committee.
"The current plan is embassy-based presence. As I take a look at conditions on the ground, when the President made that decision, it didn't account for the changes in the past two years," Campbell said.
But any modifications to the U.S. drawdown would also represent a political climbdown for Obama.
"President Obama was very clear when he set out that timeline that he would stick to that no matter what, and there was very little room to reconsider that," said Bensahel.
"He has every incentive to want the war to end in his administration on good terms," she said. "For him to be reconsidering the number of troops is clearly a political choice he does not want to have to make."
Any decision to retain U.S. troops in Afghanistan after 2016 would offer an opening to Obama critics to claim the President was implicitly admitting he had been wrong to pull U.S. troops home from another war -- Iraq -- opening a vacuum for ISIS to exploit.
Scott Smith, a former senior aide to the U.N. special representative in Afghanistan, now with the U.S. Institute of Peace, said events in recent days make Obama's decision even more complicated.
"If there is decision now to stay, it will look like an act of desperation or of panic, and as a result of Kunduz," he said. "If it had been made much earlier, it would look like an act of solidarity with a government with which we have a partnership agreement."
One difference between Afghanistan and Iraq is that the power-sharing government of President Ashraf Ghani, which Washington invested plentiful diplomatic capital in forming, desperately wants U.S. troops to stay. That was not the case under the government of ex-Prime Minister Nuri al-Maliki in Baghdad, who complicated U.S. efforts to leave a residual force.
That's one reason why the Afghan government's response to the hospital attack in Kunduz was fairly muted compared to Karzai's tirades against the many U.S. operations that caught civilians in the crossfire.
Smith said that in the end, it was possible that Obama would accept a plan to keep at least one base open in Afghanistan with up to 6,000 U.S. troops.
"The idea will be to keep them out of combat operations as much as possible -- but they will be able to hold the Afghan hands a little bit longer," he said.
But such a decision would also mean a second two-term U.S. president handing his successor a war that seems to have no end, but that Washington no longer has the desire or the resources to fight.