A high-ranking federal prosecutor was found dead inside a Southern California federal building on Wednesday, just hours after he was reported missing.

Andrew Haden, 48, the No. 2 official in the U.S. Attorney's Office for the Southern District of California, was discovered in a vacant office at the Edward J. Schwartz Federal Building, officials said.

The county Medical Examiner's Office will determine the official cause and manner of death, but a source told the San Diego Union-Tribune that investigators believe Haden died by suicide.

Haden was a 16-year veteran of the office who climbed the ranks after joining in 2010 through the Attorney General's Honors Program. Haden served as first assistant U.S. attorney and previously ran both the Violent Crimes & Human Trafficking Section and the Criminal Division. The federal prosecutor was also a U.S. Navy veteran and a father of two school-aged children.

U.S. Attorney Adam Gordon broke the news to staffers in an email Thursday.

"This is one of the darkest days in our office's history, but there was nothing dark about Andrew Haden's life," Gordon wrote. "He was a beacon of light — full of laughter, friendship, integrity and unwavering commitment to serving our community.

"We will honor his life and legacy by carrying his light forward, today and always," he added.

Even the defense attorneys who squared off against him were rattled. Jeremy Warren, who faced Haden in court time and again, told the newspaper "the fact that we remained friends throughout is a testament to the type of guy he was," calling the death "a huge blow to the entire federal community in San Diego."