Capt. Speicher's F/A-18 Hornet fighter was shot down over Iraq during Operation Desert Storm on Jan 17/91, and was listed as killed. There has been considerable controversy regarding his fate, however, and in January 2001, the Secretary of the Navy took the extremely rare step of changing his status to "missing in action." In 2002, it was changed again, this time to "missing-captured." Many also believe that his aircraft was not shot down by a surface-to-air missile, as claimed at the time, but by an Iraqi fighter that passed American planes who were not allowed to engage it. See also the March 27/01 CIA report.

After Operation Iraqi Freedom, evidence was found that included a flight suit believed to be his, an escape and evade sign located on the desert floor, and what appear to be the initials "MSS" scrawled on a wall of a cell in the Hakmiyah prison in Baghdad. Speicher's name was also found on a document in Iraq, dated January 2003, that had the names of prisoners being held in the country. Despite these efforts and clues, however, Speicher's whereabouts and the exact details of his fate remained unknown until a July 2009 tip from Iraqis led to his burial place:

"One of these Iraqi citizens stated that they were present when Speicher was found dead at the crash site by Bedouins and his remains buried. The Iraqi citizens led U.S. Marines to the site who searched the area.... The recovered remains include bones and multiple skeletal fragments. Positive identification was made by comparing Speicher's dental records with the jawbone recovered at the site. The teeth are a match, both visually and radiographically."