Operations in Florida waters and the Caribbean Sea were conducted until 15 September 1950, when she entered the Electric Boat Company yards for modernization.

Frequent trips to Guantanamo Bay, Cuba, and local operations continued until 25 May 1959, when she sailed to join in special exercises in the Mediterranean before returning to Key West on 9 August.

On 11 February 1969, Chopper was participating in an ASW exercise off the coast of Cuba with Hawkins when her electrical power tripped off-line.

Still, Ken Taylor, the senior chief petty officer in the maneuvering room, independently ordered both main motors back full.

Despite the backing bell (an order for motors full astern), blowing ballast, and other efforts to regain control of the submarine, the down angle continued to increase, and within one minute of the power failure, Chopper was nearly vertical in the water, bow down.

On 21 July, while Spadefish was on her final approach, Chopper began to take on water, broke her tethers, and sank.

In his book The Hunt for Red October, author Tom Clancy mentions the misfortune of Chopper in 1969 while discussing the fate of the fictional Soviet Alfa-class fast-attack sub E.S.

In Ice Station Zebra (novel) by Alistair MacLean there is a description of a sub that dives bow first far past its test depth, with the crew taking actions very similar to the ones taken by Chopper.