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VS-41 was originally activated in 1960 to train the crews of Grumman S-2 Tracker anti-submarine aircraft stationed on the U.S. West Coast. Two squadrons equipped with the Tracker were based each on the anti-submarine carriers (CVS) of the Essex-class to counter the threat of the large Soviet submarine fleet. In the mid-1970 both the CVS-carriers and the S-2 Tracker were phased out.
On 20 February 1974 VS-41 received the successor of the Tracker, the Lockheed S-3A Viking. The Viking-squadrons were now integrated into the former Attack Carrier Air Wings, which became Carrier Air Wings. During the latter half of the 1980s VS-41 was equipped with the upgraded S-3B. With the diminishing submarine threat after the end of the Cold War VS-41 was redesignated as a "sea control squadron" on 1 October 1993. In 1994 the squadron became responsible for the training of all U.S. Navy S-3 squadrons.