[1] In 1927, SubDiv 19 was transferred to the Battle Fleet and based at San Diego, California, with Mare Island Naval Shipyard as homeyard for its boats.

[1] S-46 departed Panama on 11 June, arrived at San Diego on 31 July, then proceeded to Pearl Harbor to participate in tactical exercises with other Battle Fleet submarines.

[1] Still in SubDiv 11, S-46 remained based at Coco Solo through the end of the decade, operating on a schedule similar to that of her first tour in the Canal Zone.

[1] In mid-April, the World War I-design submarines arrived at their new base, Brisbane, Queensland, and joined Task Force 42 (TF 42).

[1] On leaving Moreton Bay, the S-boat conducted sound training exercises with a Royal Australian Navy escort, then continued on.

[1] On 4 June, west of the Willaumez Peninsula, she developed motor trouble and turned for Vitiaz Strait, one of the few areas for which she carried charts.

[1] On 19 June, an auxiliary air compressor jammed, the motor burned out, and the resulting smoke added further habitability problems to the already hot and humid condition of the boat.

[1] From 11 September-11 October, she resumed a defensive role and patrolled in an area east of Normanby Island, Papua New Guinea in anticipation of a major enemy attack of Milne Bay.

[1] After the cessation of hostilities in August, she was ordered to San Francisco, California, for inactivation, and in late September, she moved up the bay to Mare Island Naval Shipyard.

[1] Her name was struck from the Naval Vessel Register two weeks later, and her hulk was sold for scrapping to the Salco Iron and Metal Company, San Francisco, in November 1946.