John F. Fagan Jr., 78, a retired Navy captain who was a commanding officer of nuclear submarines and a strategic weapons aide at the Pentagon, died of congestive heart failure Sept. 17 at a convalescent center in Newport News, Va.  Capt. Fagan, who lived in Annandale for 34 years before moving to Williamsburg in 2001, was a native of New Orleans and a graduate of the U.S. Naval Academy in Annapolis. He received a master's degree in nuclear physics from the Massachusetts Institute of Technology.

During the early part of his nearly 30-year career in the Navy, Capt. Fagan was commanding officer of the nuclear submarines USS Lewis & Clark and the USS Shark. His other command assignments placed him in charge of the Navy's submarine development group No. 2 in New London, Conn., and the U.S. Navy Nuclear Power School in Vallejo, Calif. At the Pentagon, Capt. Fagan was military assistant to the assistant  director of offensive strategic weapons in the office of the director of defense research and engineering. He retired from active military duty in 1971 and became a senior scientist and senior vice president of defense contractor Systems Planning Corp. in Reston. He worked for the company for 17 years.

His wife of 56 years, June Heiderich Fagan, died in 2001. Survivors include three sons, Jon H. Fagan of Newport News and Jay S. Fagan and Jeffrey Fagan, both of Orange Park, Fla.; four grandchildren; and a great-grandson.