Lt Col Francona enlisted in the Air Force in 1970, and served as a Vietnamese linguist until 1973, conducting aerial reconnaissance missions over Vietnam and Laos.  After Arabic language training, he served at a variety of locations in the Middle East from 1975 to 1977, and supported the evacuation of the U.S. Embassy in Beirut, Lebanon in 1976.  In 1978, he became an Arabic language instructor at the Defense Language Institute in Monterey, California.

Following his commissioning in 1979, Lt Col Francona was an instructor at the Air Force intelligence school in Denver, Colorado.  From 1982 to 1984, he was a Middle East operations officer with the National Security Agency.  In 1984, he was assigned as an advisor to the Royal Jordanian Air Force in Amman, Jordan.

In 1987, Lt Col Francona was assigned to the Defense Intelligence Agency as the assistant Defense Intelligence Officer for the Middle East.  During this assignment, he spent much of 1987 and 1988 at the U.S. Embassy in Baghdad, Iraq, as a liaison officer to the Iraqi armed forces directorate of military intelligence. Lt Col Francona traveled extensively as an observer of Iraqi combat operations against Iranian forces, and flew sorties with the Iraqi air force.

Immediately following the Iraqi invasion of Kuwait in August, 1990 and through the Gulf War, Lt Col Francona was deployed to the Gulf as the advisor on Iraqi armed forces and personal interpreter to commander in chief of the U.S. Central Command, General Norman Schwarzkopf.  As such, he was the lead interpreter for ceasefire talks with the Iraqi military at Safwan, Iraq, in March, 1991.

After the end of the Gulf War, the colonel served in the Office of the Secretary of Defense, and was a principal author of the Department of Defense report to Congress on the conduct of the Gulf war.  In 1992, he was selected to be the first air attaché to the U.S. Embassy in Damascus, Syria, returning to the United States in early 1995. 

From 1995 to 1996, Lt Col Francona served with the Central Intelligence Agency, and participated in a variety of sensitive operations in the Middle East, including the escape of an Iraqi scientist's family.  During one of these operations, he survived an attempt on his life by Iraqi intelligence service agents. 

In 1996, the colonel was selected to develop the Department of Defense counterterrorism intelligence branch.  In late 1997, the colonel led a special operations team supporting NATO forces in Bosnia.  He returned to the United States and retired from active duty in 1998.

Since retiring from the Air Force, Lt Col Francona has written Ally to Adversary: An Eyewitness Account of Iraq's Fall from Grace, and consulted with government and private firms.  Currently he is a media analyst on Middle East political-military events, currently under contract to NBC News, and appears regularly on NBC Nightly News, The Today Show, MSNBC, CNBC, Hardball, Countdown, and others.

The colonel has a bachelors degree in government and the Arabic language, and a masters degree in international relations with a concentration in Middle East studies.  His decorations include the Defense Distinguished Service Medal, the Bronze Star, and nine Air Medals, as well as campaign awards for service in Vietnam, the Persian Gulf, and the Balkans.  The colonel was awarded the Central Intelligence Agency Seal Medallion for his service with that agency.  In 2006, Lt Col Francona was inducted into the Defense Language Institute Hall of Fame.

Lt Col Francona and his wife Emily reside on the Oregon coast.