Air Force Mortuary Affairs Operations - AFMAO - is the unit that runs the Dover mortuary. The official mission statement frames the work as a sacred commitment to ensure dignity, honor, and respect to the fallen, and care, service, and support to their families. The staff prepares the remains of U.S. service members, government officials stationed abroad, and their families. The facility houses the largest mortuary under the Department of Defense and the only DoD mortuary in the continental United States. AFMAO became a named activity in December 2008 and a Field Operating Agency in May 2014, reporting directly to Headquarters Air Force. The organization now operates from Dover, Ramstein Air Base in Germany, Joint Base Pearl Harbor-Hickam in Hawaii, and Yokota Air Base in Japan - a global network designed to receive remains from any combatant command and route them through Dover for the final care.

The Dover mortuary has been called on for the largest American casualty events of the last fifty years. In 1978, after the Jonestown mass murder-suicide in Guyana - in which more than 900 people died, most of them American citizens - the remains came to Dover. In 1986, when the Space Shuttle Challenger broke apart 73 seconds into flight, killing all seven astronauts including the schoolteacher Christa McAuliffe, their remains were identified at Dover. In 2003, after the Space Shuttle Columbia broke apart on re-entry, again killing all seven crew, Dover received them again. After the September 11, 2001 attacks, Dover became a primary site for identifying military and civilian personnel killed at the Pentagon and elsewhere. The mortuary's work in these cases - careful, professional, conducted under intense public attention - earned the facility a reputation as one of the most expert forensic and ceremonial operations in the world. Most of the staff are civilians. Many have spent careers there. The work is too heavy for short tours.

In 2011, the United States Office of Special Counsel found that the Dover mortuary had committed what investigators called gross mismanagement of remains between 2004 and 2008. The investigators documented specific failures: body parts had been lost; the damaged arm bone of a deceased soldier had been sawed off without telling the family so the body could fit in a casket; supervision had been lax. Three supervisors were disciplined but kept their jobs. The Special Counsel investigation found that Air Force officials had tried to silence whistleblowers, falsified records, and lied to investigators. Colonel Robert H. Edmondson, who commanded the facility from January 2009 to October 2010, was reprimanded and fined $7,000 but allowed to remain in the Air Force. Quinton Keel, the division director, was demoted and reassigned before eventually resigning. The Special Counsel was critical of the Air Force for failing to remove personnel. The USAF convened a board led by General John Abizaid, the former CENTCOM commander, to review the mortuary's operations.

In December 2011, a Washington Post investigation revealed that between 2004 and 2008, the Dover mortuary had disposed of the partial cremated remains of 274 U.S. military personnel in the King George County Landfill in Virginia. The remains were the unidentifiable fragments left over after primary remains had been returned to families - the small pieces that forensic identification had not been able to attribute. The families had not been told. Many had assumed the partial remains had been given a respectful disposition. The landfill was a working commercial landfill. In February 2012, the Post revealed that mortuary and Dover officials had suggested burying the remains at sea but were overruled by an unidentified Air Mobility Command officer and Army Personnel Command officers, who directed that the remains be disposed of as medical waste. The decision had cascaded through years of operations. Mortuary procedures changed after the disclosures. The remains buried in landfills are not recoverable; the families affected received apologies but no remediation.

The 2011 investigations came to light because of civilian employees at the Dover mortuary who refused to stay quiet. The Office of Special Counsel found in January 2012 that mortuary officials had retaliated against four civilian whistleblowers - two were fired, two were suspended - for their role in raising concerns. In June 2012, three of those whistleblowers - James G. Parsons Sr., Mary Ellen Spera, and William Zwicharowski - were honored as Public Servants of the Year by the United States Office of Special Counsel. The honor recognized that they had risked their careers to expose practices that violated the sacred commitment the mortuary was supposed to embody. The Dignified Transfer ceremony - the slow walk from the aircraft to the transfer case, the family members watching from a private observation room - is the public face of Dover's work. The whistleblowers reminded the public that the private face mattered too. Their testimony forced reforms in chain-of-custody procedures, identification protocols, and family communication. The facility's reputation has slowly rebuilt itself in the years since. Most American service members killed overseas still come home through Dover. Many families now know how carefully their loved ones are received.