[2] The action moves back and forth between the characters against the backdrop of World War II: Victor "Pug" Henry takes part in various battles while separating from his wife.

Byron's wife Natalie is trapped in Axis territory with her uncle, celebrated author Aaron Jastrow, and another major strand focuses on their story as Jews caught in Europe.

As Byron attempts to find out what is happening to them, eventually tracking them down amidst the chaos of wartime Europe, the story of the Holocaust is gradually revealed to the American government and people.

Another plot thread concerns Aaron Jastrow's cousin Berel who is captured near the end of The Winds of War and is forced to join Kommando 1005, SS officer Paul Blobel's Jewish contingent that travels around Eastern Europe exhuming the bodies of massacred Jews and disposing of them in an effort to hide the evidence of Nazi mass murder.

One frequently cited criticism of the plot is that Wouk's repeated references to history take precedence over character development as well as the observations and ideas he offers to explain WWII in a larger context.

"[5] Another critic noted that in regards to the novel's depiction of the holocaust, that it may be a serious "trivialization of history to employ old fashioned tricks of plotting, such as the chapter-ending cliffhanger, in dramatizing such grave events".

[9] At the end of the novel, Wouk wrote that his purpose was to "bring the past to vivid life through the experiences, perceptions, and passions, of a few people caught in the war's maelstrom.