The submarine stood out of Midway on 16 March 1944 on her second war patrol but encountered no Japanese targets during her 42 days at sea, mostly near the Palau Islands.

She prowled the waters off Honshū for more than a month without bagging any enemy ships, and returned to Pearl Harbor on 29 September, after 53 days at sea.

On 28 November, she received word that no air raids would be launched that day, giving her carte blanche to roam the waters near Tokyo Bay.

Enright deliberately set the torpedoes to run shallow (10 ft or 3 m) in hopes of capsizing the target by holing it higher up on its hull.

The damage was magnified by the fact that Shinano had turned south just minutes before Enright loosed his torpedoes, thus exposing her entire side to Archerfish—a nearly ideal firing situation for a submarine.

While her officers and crew spent the holidays at a rest and recreation camp located on Guam, Archerfish underwent refit at the island.

She damaged one unidentified target and claimed a submarine on 14 February 1945[11] during this patrol which ended on 3 March, three days earlier than scheduled, due to bow-plane problems.

Archerfish touched at Saipan and Pearl Harbor before arriving back in the United States at San Francisco, California on 13 March.

Archerfish was one of 12 submarines that entered Tokyo Bay on 31 August, and moored alongside Tender USS Proteus (AS-19), near the Yokosuka Navy Yard.

However, a fire broke out in her maneuvering room on 28 March, and the ship returned to Mare Island under her own power for a restricted availability to have the damage corrected.

Commander George F. Bond and Chief Engineman Cyril Tuckfield safely completed a 52-second, 302-foot buoyant ascent from the forward escape trunk.

[12] In early 1960, Archerfish was chosen to participate in Operation "Sea Scan", a scientific study of marine weather conditions, water composition, ocean depths, and temperature ranges.

On the cruise, the submarine visited Portsmouth, England; Hammerfest and Bergen, Norway; Faslane, Scotland; Thule, Godthaab, and Julianehab, Greenland; Belfast, Northern Ireland; and Halifax, Nova Scotia, before mooring at New London on 3 December.

After six weeks of upkeep, Archerfish got underway on 20 January 1961 for the Pacific phase of "Sea Scan", transited the Panama Canal on 6 February, and proceeded via San Diego to Hawaii.

She then commenced phase three of "Sea Scan" in the eastern Pacific area, with stops in Pearl Harbor and Midway Atoll, and returned to San Diego for the Christmas holidays.

Following two and one-half months of operations she returned to the United States for a brief visit to San Francisco, California, before reentering Pearl Harbor early in May.

Late May and most of June were devoted to surveying off the northwest coast of the United States and Canada, with port calls in Portland, Oregon; Seattle, Washington; and Vancouver, British Columbia.

The submarine was back in Yokosuka for drydocking in July and August before beginning three months of continuous surveying in the mid-Pacific, broken only by brief fuelling and upkeep stops at Midway and Pearl Harbor.

She departed Yokosuka on 25 November, for an extended cruise to the southern hemisphere, arrived in Australia in mid-December and took a three-week holiday in Newcastle and Sydney.

From the latter port, Archerfish travelled to Guam for a two-week upkeep in late January 1964 and finally reached Pearl Harbor on 5 March.

Archerfish began an extended fourth and final phase of Operation "Sea Scan" when she left Pearl Harbor on 17 June, and headed for the eastern Pacific.

She made port calls during July at Seattle and Olympia, Washington, and returned to Pearl Harbor on 19 August, for a three-week upkeep and drydocking before undertaking a cruise to the South Pacific.