Berquist won a narrow victory for the nomination with 33% of the primary vote—taking roughly the same number of votes he had received in the 1934 general election.

In the Assembly, Berquist rose to junior floor leader for the Progressive caucus and was appointed secretary of the special joint investigative committee on land utilization in the northern area of the state.

Nelson, however, had already been appointed to the federal War Production Board and, on the eve of the Progressive Party state convention, declined the nomination.

[11] Prior to the Attack on Pearl Harbor, the Progressive Party had a staunch non-interventionist policy and insisted that America's best strategy in this era was to build up domestic strength.

[12] However, just weeks after his defeat in the 1942 election, Berquist resigned his Assembly seat and enlisted in the United States Army for service in World War II.

While at Fort Riley, he wrote to his teenage son explaining the reasons for his absence and his rationale for the war in a widely reprinted letter.

He spoke about the atrocities of the Germans, encouraged them to support veterans of the war, and gave an exhortation that there must be "no breakdown of democracy in the United States.

The move was led by longtime Progressive United States Senator Robert M. La Follette Jr., who saw unification with the Republican Party as his only path to re-election.

Berquist announced his candidacy in an open letter to Senator La Follette in which he explained that Roosevelt, Truman, and Wallace were far more aligned with the Progressive Party's ideals than the Republicans.

[21] La Follette went on to lose the Republican nomination to Joseph McCarthy, and Berquist was defeated in the general election by incumbent Alvin O'Konski.

Following his defeat, Berquist became involved in the newly reorganized national Progressive Party, which had been formed around former Roosevelt Vice President Henry A. Wallace.

In his announcement, he asserted that Wallace and the new Progressive Party were the true heirs to Roosevelt and the New Deal which he said was being derailed and reversed by the efforts of Southern Democrats and "northern big city political machines."

He pointed to the emerging crisis of the new Cold War and the nuclear arms race, the resultant massive expansion of defense spending, the resumption of the military draft, new curbs on labor rights, price inflation, abrogation of civil rights for African Americans and political minorities, and a housing crisis.