Relieved of command of Charleston on 12 December 1898 by Capt. W. H. Whiting, Glass returned to the United States and soon assumed command of the naval training station at San Francisco, California, on 23 January 1899. Promoted to rear admiral in 1901, he broke his flag in the armored cruiser on 4 February 1903 as Commander-in-Chief, Pacific Squadron. During his tour of duty in command of the squadron, the flagship, New York, together with the cruiser and screw steamer visited Adak and Kiska, in the Aleutian Islands, conducting surveys of the latter place in July 1903 with an eye toward establishing a coaling station there.