Pendergrast was one of twenty-six sailors ordered by John D. Sloat to pursue the pirate Roberto Cofresi and force his ship aground in Puerto Rico, which led to his capture.

[9] On September 24, 1860, Pendergrast sailed from Philadelphia aboard the sloop Pawnee in order to assume command of the Home Squadron, then operating off the coast of Mexico.

[10] At the outbreak of the American Civil War in 1861, Pendergrast was in command of the frigate Cumberland at anchor near the Gosport Navy Yard awaiting repairs.

[11][12] Pendergrast positioned the Cumberland off the harbor to either defend it or protect the escape of Federal ships.

[13] Most of the blame for the loss of the Gosport Navy Yard fell to Charles Stewart McCauley although some of it was also placed on Pendergrast who controlled the Federal fleet on the Atlantic coast.

[2] Upon the Secession, she reportedly refused to accompany her husband in his allegiance to the United States and swore she would never live with him again.