San Francisco joined Submarine Force US Pacific Fleet following an initial shakedown cruise, and moved to her homeport at Pearl Harbor.

[3] On 8 January 2005 at 02:43 GMT, San Francisco suffered a collision with an undersea mountain about 364 nautical miles (675 km) southeast of Guam while operating at flank (maximum) speed at a depth of 525 feet (160 m).

Ninety-eight crewmen were injured, and Machinist's Mate Second Class Joseph Allen Ashley, 24, of Akron, Ohio, died from head injuries on 9 January.

The Navy concluded that "several critical navigational and voyage planning procedures" were not being implemented aboard San Francisco, despite Mooney's otherwise remarkably good record.

The Navy determined that information regarding the seamount should have been transferred to the charts in use – particularly given the relatively uncharted nature of the ocean area that was being transited – and that the failure to do so represented a breach of proper procedures.

Nonetheless, a subsequent study by UMass Amherst indicated that the Navy's charts did not contain the latest data relevant to the crash site because the geographical area was not a priority for the Defense Mapping Agency.

"[9][4][page needed] San Francisco had recently replaced her nuclear fuel and she was thus expected to remain in service until 2017, so the Navy determined that repair of the submarine was in its best interests.

San Francisco steamed to Puget Sound Naval Shipyard (PSNS) in Bremerton, Washington via Pearl Harbor, Hawaii, where she arrived on 26 August 2005.

The dry-docking project involved cutting more than one million pounds (450 tonnes) of forward ballast tanks and sonar sphere off the former USS Honolulu and attaching them to San Francisco.