There are a few clear, powerful themes in Stanton's historical narrative about the sinking of the USS Indianapolis during World War II.

The predominant theme throughout the novel is the astounding sacrificial courage of soldiers. Throughout the book, Stanton recounts conversations and situations in which the crewmen of the ship consistently displayed sacrificial courage, as Stanton provides first-hand accounts of men's bravery before, during, and after the tragic event at sea. Sailors and officers alike risked their lives for their nation and their fellow crewmen by joining the Navy during wartime, sailing into enemy territory, helping survivors endure dangerous Pacific waters, and dealing with the impact of the event years later.

Another clear theme of this book is honor. In his extensive research of this event, Stanton uncovered unsettling accounts of how the ship's captain, Captain Charles McVay, was initially court-martialed and blamed for the sinking of the USS Indianapolis, despite many wartime circumstances and communication with military officials that was not duly considered. Through many efforts, including Stanton's tireless months of interviews with survivors, Captain McVay was exonerated in 2000. The honor of the crewmen and the captain was highlighted by Stanton's accurate, detailed, and compelling accounts of the tragic event during the war.

Therefore, the theme of justice is also present in the novel, as Stanton seeks to set the record straight for both the captain and his crew. While the Navy and government also did not want to bring attention to the delayed rescue of the crew in the Pacific, Stanton's detailed accounts of crew members' incredible fight against hypothermia, shark attacks, sickness, injuries, and imminent death forced public recognition of the tragic circumstances.

Likewise, the theme of brotherhood (bond of soldiers) is also apparent in the novel. Throughout the stories and accounts in the novel, there is an unmistakable bond that runs deep and everlasting between the crew members of the USS Indianapolis, as survivors remembered those who lived, laughed, served, fought, survived, and died next to one another.