The move follows the unexpected sudden retirement of Adm. Bill Moran, who had already been confirmed as next CNO.
Chief of Naval Operations Adm. John Richardson is meeting with his Chinese counterpart this week in Beijing.
U.S. freedom-of-navigation operations are a challenge to Chinese territorial ambitions in the South China Sea.
Sortie Condition Bravo was set on Saturday, indicating the onset of destructive weather conditions within about 48 hours.
The old Hunters Point Naval Shipyard is contaminated with radioactivity and industrial pollutants.
A Naval Board of Inquiry found that the attack by Israeli warplanes on the intelligence-gathering ship was an accident.
The Navy eliminated the Second Fleet command structure in 2011 as a cost-saving measure .
China says the islands are mainly for civilian purposes and to boost safety for fishing and maritime trade.
The guided-missile destroyer departed Yokosuka on Saturday morning aboard the heavy-lift vessel MV Transshelf.
The hospital ship USNS Comfort has ended its relief effort in Puerto Rico for the victims of Hurricane Maria.