Like a good novel, The Perfect Storm returns to a series of general ideas evoked by the particular situations endured by its characters. The main theme might be summed up in the old cliche, "men against the sea," but Junger imbues this venerable idea with numerous contemporary relevancies. Primary is the aforementioned stress on the unchanging danger of fishing at sea and the unrecognized continuity between the days of sail and modern steel and diesel technology. Quotes from Samuel Johnson, Melville's Moby Dick, and the Bible make this point by linking the ancient and the new: the human risks and terrors endured by fishermen have changed little if at all. Nature is still unconquerable by the pitiful efforts of men; though the connection is established only indirectly, the confidence and even arrogance that declared the Titanic unsinkable is still at work in captains like the owner of the Sartori, who insists his small sailboat can survive hurricane force winds and waves. In the case of Bob Brown, the owner of the Andrea Gail, such confidence in human power is entangled with the profit motive, which dictates scores of small decisions (Should stability be risked against extra fuel-carrying capacity?) which cumulatively can put a boat in an irrecoverable situation. Part of Junger's argument against the conventional idea that "fate" governs deaths at sea is that in fact fate is shaped by countless small choices, most of which seem trivial at the time they are made.

Like Brown, captain Billy Tyne is sure of his boat and his ability to find a way out of peril; however, he risks his own life as well as those of his men if he goes a step too far. All the crewmen are putting themselves at risk to escape poverty or dysfunctional lives on shore; Junger asserts that none would choose fishing if other options were available. A mitigating factor, however, is the camaraderie enjoyed by the fishermen at work and onshore, for, once in the life, they seem unable to escape each other's company even in barroom celebrations. Fishing provides a powerful identity and gives pride to men who have little education or privilege.

This identity, however, can be the despair of the wives and families. Divorce is common among men who spend weeks and months at sea, and the women who love them are both attracted to their toughness and uncomplaining competence and terrified at the prospect of becoming widows, unsure even if their loved ones are truly dead. For the most part, fishermen simply disappear; there are often no bodies to bury and funerals to signal their end. Junger is very good at capturing the farflung effects of the storm. Just as tiny ripples in the Caribbean can eventually become hundred-foot waves off New England, so the human consequences, personal and social, can have effects far distant from their source. The general theme of the interconnectedness of nature is thus applied to human nature as well: "Like a war or a great fire, the effects of a great storm go rippling outward through webs of people for years, even generations. It breaches lives like coastlines and nothing is ever again the same."

Another theme is the casual heroism of rescue workers. Parajumpers, pilots, rescue swimmers, and aircrews, all train for years to go to the aid of complete strangers under appalling weather conditions. By following the actions of a couple of rescue operations during the storm, and by briefly sketching some of the life stories of the crews, the book allows the reader to form a picture of the kind of people who would choose such careers and the enormous sacrifices some make. This kind of heroism is rarely celebrated in popular culture, and Junger sees his task as making readers understand its nature.