During the Virginius Affair crisis, the United States had ordered that not only the North Atlantic Squadron sail to Key West, Florida, but also the South Atlantic and European squadrons. All had arrived by 4 February 1874, but by then the crisis was over.
With all those ships gathered in one point, it was decided to hold the first multi-ship, open-ocean tactical exercise in U.S. Navy history. To avoid problems with who ranked who, Scott was ordered to take his flagship, the USS Worchester on a special cruise to Cuba and the Winward Islands to assess and report on the conditions after the Virginius Affair.
Scott turned over command of the North Atlantic Squadron to Rear Admiral J.R.M. Mullany on 13 June 1874 and retired the same day, having reached mandatory retirement age of 62.
The admiral lived in Washngton, D.C., after that and died 23 March 1882. He was first buried at Washington's Oak Hill Cemetery, but in 1896, his remains were exhumed and reburied at Arlington National Cemetery.