To me the story is about what happens off the submarine.
In Part 1: the story events on boat set up character for the Captain's action and his decision's after the primary mission. I thought it was well told but similar to other submarine WW2 books.
In Part 2: The plot weaving a brutal story of survival. All his actions after the attack mission, his feeling of hopelessness. Japans illogical refusal to admit the war was lost. The brutality of humans and also the spirit of human spirit.
In Part 3: The "discussion" and "reaction" of the USN to the Captain's story after the war is over; this is what made me pause and think. Although I was never in the military, the story has made me wonder how much of this adjuicate behavior went on.