[4] Franks missed 3+1⁄2 seasons during World War II, when he served in the United States Navy in the Pacific Theater of Operations and attained the rank of lieutenant (junior grade).

In August of that season, however, he resigned his post to return to the Major Leagues as a backup catcher with the Philadelphia Athletics, where he appeared in 48 games in 1947–48 and batted .221.

According to author Joshua Prager in his 2006 book The Echoing Green, Franks played a critical role in the Giants' Bobby Thomson's famous pennant-winning home run in the 1951 NL tiebreaker playoffs—Baseball's Shot Heard Round The World.

He also spent two additional one-year terms (in 1958 and 1964) as a San Francisco Giants coach before succeeding Alvin Dark as the club's manager a half‐hour after the conclusion of the 1964 season on October 4.

[11] A highly successful businessman off the field, Franks spent the next eight years out of the Major League spotlight, apart from a partial season (August and September 1970) as a pitching coach under Durocher with the Chicago Cubs.

[12] In 1977, he led the Cubs back to the .500 level, but the team lost ground in 1978 and was just one game above the break-even mark in September 1979 when Franks resigned (issuing a number of complaints about certain players).

He was replaced by Dallas Green just under five months later on October 15 as part of the franchise ownership transition from William Wrigley III to Tribune Company.