Following an overhaul at San Francisco 1 May – 26 July 1958, the warship's home port was changed to Guam and "Lewis" sailed to her new station on 14 October, arriving in Apra harbor on 1 November. She conducted island patrol and search-and-rescue operations there for most of the next year, interspersed with port visits to Subic Bay and Hong Kong in mid-April 1959. During the summer and fall "Lewis" conducted survey work, helping map the deep waters of the region. Starting in November 1959 she took part in Project Nekton, a series of deep dives in the Mariana Trench by "Trieste", a deep-diving research bathyscaphe purchased by the Navy the previous year. On 23 January, "Lewis" helped track "Trieste" with her sonar gear as the bathyscaphe conducted the deepest manned dive ever undertaken, to the bottom of trench Challenger Deep below the surface.