By Cora Currier, ProPublica

Soon after taking office, President Obama pledged to open a new inquiry into the deaths of perhaps thousands of Taliban prisoners of war at the hands of U.S.-allied Afghan fighters in late 2001.

Last month, the White House told ProPublica it was still “looking into” the apparent massacre.

Now it says it has concluded its investigation – but won’t make it public.

The investigation found that no U.S. personnel were involved, said White House spokeswoman Caitlin Hayden. Other than that, she said, there is “no plan to release anything.”

The silence leaves many unanswered questions about what may have been one of the worst war crimes since the U.S. invasion of Afghanistan, including why previous American investigations were shut down, and how evidence was destroyed in the case.

“This is not a sufficient answer given the magnitude of what happened here,” said Susannah Sirkin, director of international policy for Physicians for Human Rights, the organization that originally uncovered mass graves where the prisoners were buried.

The long saga began in November 2001, when Taliban prisoners who had surrendered to Northern Alliance commander Abdul Rashid Dostum were transported in shipping containers without food or water. According to eyewitness accounts and forensic work by human rights investigators, hundreds of men died of suffocation while others were shot, and their bodies buried at the desert site of Dasht-i-Leili.

Dostum was working closely with U.S. troops at the time. Surviving prisoners alleged that Americans were present at the loading of the containers – but the Pentagon has said repeatedly that it had no evidence that U.S. forces participated or were even aware of the deaths. (Dostum has denied any personal involvement, and claims that roughly 200 men died in transit, from battlefield wounds.)

In the fall of 2002, the U.S., U.N., and even Dostum himself expressed support for an investigation. But none got underway. In the summer of 2009, prompted by a New York Times report that Bush administration officials had actively discouraged U.S. investigations, President Obama ordered a new review of the case.

Hayden, the White House spokeswoman, said the new investigation “was led by the intelligence community,” and found that no Americans – including CIA officers, who were also in the region – were involved.

She declined to answer the following lingering questions:

What was the scope of the investigation? Former Bush administration officials who had been involved in the initial U.S. response to Dasht-i-Leili told ProPublica that they had not been contacted for a new inquiry.

Physicians for Human Rights said it received only tepid responses to its queries from the administration over the past several years.

Did the investigation cover the allegations, reported in the New York Times, that Bush administration officials had discouraged inquiries by the FBI and State Department?

Did the U.S. help with related inquires by the U.N. or the Afghan government? Even absent direct involvement of U.S. personnel, government documents make clear that the U.S. knew about the allegations early on. The U.S. was in an alliance with Dostum, and was the de facto power in the country after the invasion. An Afghan human rights official told ProPublica last month, “I haven’t seen any political or even rhetorical support of investigations into Dasht-i-Leili or any other investigation into past atrocities, from either Bush or Obama.”

Did the new investigation cover revelations that graves were disturbed and evidence removed as late as 2008? What, if anything, did the U.S. do to help protect the site over the years?

A parallel investigation began by the Senate Foreign Relations Committee in 2010 also never made headway. The committee staffer leading that investigation was former CIA officer John Kiriakou, who is currently serving time in federal prison for revealing the name of an undercover officer to a reporter.

In letters from prison to ProPublica and an interview published recently in Salon, Kiriakou said that Secretary of State John Kerry, who was then chairman of the committee, personally called off the investigation. The State Department declined to comment, but a former Senate aide to Kerry called Kiriakou’s account “completely fabricated.”