In response to questions, the Pentagon said it was able to provide only limited information — confirming that Bergdahl was the missing soldier referred to in the emails — citing the number of years since the event had happened.

Petraeus has condemned the use of torture and the abuse of detainees in US military custody. One of the most eminent generals in a generation, he ended his career in disgrace after he was found guilty of improperly sharing classified information with his biographer turned lover, Paula Broadwell, and resigned as the CIA director. Although Petraeus is still on probation after pleading guilty to mishandling classified information in April of 2015, his career could be rehabilitated by Donald Trump, who is considering appointing the general as the nation’s top diplomat.

The 2009 decision to forgo an autopsy underscores running concerns over treatment of detainees under the Obama administration. Obama came into office promising to overhaul the controversial practices that defined the Bush administration’s counter-terror policy. An earlier BuzzFeed News investigation revealed more than 300 allegations of detainee abuse in detention facilities in Afghanistan from 2011 to 2012, a trend some human rights activists fear was the norm throughout the Obama administration’s tenure.

The emails were obtained through a Freedom of Information Act lawsuit brought by BuzzFeed News against the Pentagon seeking information about detainee abuse in Afghanistan. The photos were not included in what has been released to BuzzFeed so far.

It is unclear from the records which units were involved in the mission, but one email describing the events appears to be signed by the commander — whose name is redacted — of “Red Squadron.” It’s been reported that the Red Squadron is the Navy SEAL unit that later killed Osama bin Laden, and that it is part of the storied SEAL Team Six. The Department of Defense cited privacy in redacting the commander’s name.

The death of the detainee and the push to avoid an autopsy have not been previously reported. The Pentagon emails say he died at a base, after being taken into custody by US commandos following a failed raid to rescue missing US Army Sgt. Bowe Bergdahl, who had just been captured. The commandos said the detainee died of cardiac arrest after struggling.

Petraeus, reached through an associate, declined to comment on the incident, saying he had no recollection of it.

Petraeus and other top military officials pushed to waive the autopsy that would have determined the man’s cause of death, in order to forestall protests by upset Afghans. But, emails show that a troubling series of photos emerged that showed the man’s bruised and bloody corpse, his mouth bandaged shut, which prompted another general to second-guess the decision to not conduct an autopsy that would have investigated whether the man had suffered abuse in US custody.

The detainee, according to sources in Afghanistan, was an influential tribal leader in his late fifties.

WASHINGTON — When an Afghan detainee died mysteriously in the custody of elite US forces in 2009, General David Petraeus — who has been under discussion for the role of Secretary of State — helped ensure there would be no autopsy, despite a medical examiner’s conclusions that “injurious conduct” by US troops contributed to the man’s death, according to emails obtained by BuzzFeed News.

According to the emails, Army criminal investigators looked into the man’s death, but the results of that investigation are unknown. A spokesman for the Army Criminal Investigation Command said he did not have a way of researching old case files like this quickly.

None of the high-level officers contacted by BuzzFeed News — including Gen. Stanley McChrystal and retired Adm. Bill McRaven — would comment on the incident.

“It’s part of a long-standing pattern of insufficient care and detail to legitimate evidence of detainee abuse and deaths in custody,” said Raha Wala, director of national security outreach at Human Rights First, a DC-based human rights group. “It is disappointing to see officials not take these allegations seriously.”

The emails obtained by BuzzFeed News show that in the early morning of July 2, 2009, US special forces set out on a rescue mission to search for Bergdahl, the Army sergeant who two days earlier had walked off his base in Paktika province.

The rescue team did not find Bergdahl — who would be held by Afghan militants until 2014, when he was released in a prisoner exchange and later charged with desertion — but they did take into custody the man, unnamed in the records obtained by BuzzFeed News, who they believed was a possible lead. The commandos flex-cuffed him and took him in a helicopter back to their base.

A commander cited in the emails said the man was “extremely aggressive and non-compliant” and “intentionall [sic] and repeatedly falling to the ground.” After arriving at the detention facility, the man walked “under his own power” from the helicopter into a detention facility. At this point, the commander wrote, “he increased his combative attitude until overcome by cardiac arrest.”

Despite attempts to revive the man, including CPR and chest tubes, the commander said he was pronounced dead at the scene.

In Afghanistan, sources tell BuzzFeed News the detainee was Siraj Akhunzada, an influential tribal leader aged around 55 to 60 (Afghans often lack birth certificates and don't know their exact age.) The Americans took him into custody in the village of Segana. Because Akhunzada was so prominent, there were protests against his capture. One village source, Khan Mir Hakimy, who is the head of the Tribal Affairs Department in Paktika province, said that the governor of Paktika province was contacted, and the issue went all the way up to the office of Afghanistan’s president.

The email chains obtained by BuzzFeed News indeed show that US officials felt under pressure from the Afghan government about the case. “Need to have available the full summary of the Mission, Outcome, Circumstances surrounding the death and other pertinent factors...which we know will be key questions President Karzai will be expected to have,” wrote one general.

The emails show that military brass believed the man’s death might escalate into a diplomatic incident. One general said that the governor of Paktika province demanded that the man’s body be returned to his family quickly. Military officials wanted to quickly release the body to calm things down.

Though the special operations soldiers said the man simply died of cardiac arrest, not everyone in the US military believed the troops had acted properly. According to an email written at the time by Brigadier General Raymond Thomas, there was a “non-concurrence” from the Office of the Armed Forces Medical Examiner, who “concluded that injurious conduct is a contributing factor.” The email said the official medical examiner cited his continuing concerns over allegations of detainee abuse at the hands of US troops.

Thomas is currently the commander of US Special Operations Command, SOCOM.

Another Army general, David Rodriguez, weighed in: “There are many people involved who are hearing rumors or imagining what might have happened.” He argued that “the medical examiner’s office will always take the same position.”

Gen. Petraeus authorized special operations commanders to request a waiver to the autopsy. The request, according to the emails, went up to an unnamed deputy secretary of defense.

But even the unnamed deputy secretary of defense, who was the only defense official who could approve the break in protocol, hesitated in waiving the autopsy, according to the emails. The deputy secretary sat on the request and pushed officials in Afghanistan to see if there was a way to expedite an autopsy and conduct one without relocating the detainee’s body.

In separate emails, those defense officials lament what they say is the pointlessness of an autopsy anyway.

“A US autopsy would not impress any suspicious Afghans on this,” McChrystal wrote to several officers, including Petraeus.

Defense officials in Afghanistan quickly told the secretary’s office an onsite autopsy was impossible. The official then waived the autopsy and approved the return of the man’s body to his family.

Hours later, though, photos of the body — taken 16 hours after the man had died — were passed up the chain of command. Though the photos were not released to BuzzFeed News, they are described in an email written by a commando leader, in an email forwarded by Admiral William McRaven, the commander of Joint Special Operations Command, to Petraeus, McChrystal, and others.

The emails detail that the body was covered in dried blood, bruises, and cuts, which the commander said were from “chest tubes” and “large gauge IV catheters.” The bruises, he wrote, appeared after the man died. The man’s ribs were fractured, which the commander said was from CPR to resuscitate him. His hands were tied behind his back — something the commander said was done after the man died: “Hands had been tied by the medical team post-mortem.” His mouth was bandaged shut, which the commander wrote was also done after his death, writing that the interpreter had requested this.

“All marks on the body are consistent with medical treatment administered,” the commander wrote.

But at least one general seemed disturbed by what he saw.

“I had not seen the photos when I provided my initial recommendation to forego the autopsy,” McChrystal wrote to Petraeus, after he had seen the photos and the Red Squadron commander’s descriptions.

“Absent this accompanying explanation, would not have made that recommendation,” McChrystal wrote, referring to the Red Squadron commander's description of the photos. “With the details below, it still appears to have been the right move.”

Petraeus, in the emails, did not say whether he had any similar second thoughts.

Aimal Yaqubi contributed reporting from Afghanistan.