In February, 1945, one of the fiercest battles of the Pacific theater of World War II occurs on the island of Iwo Jima. Here was taken one of the most famous photographs in history, by  photographer Joe Rosenthal, showing an American flag raised by six soldiers atop the highest point, Mount Suribachi.  Flags of our Fathers is telling the story behind this pictures, and at the same time, of the contradictions of war itself.

The movie start with writer James Bradley, son of  John "Doc" Bradley (Ryan Phillippe), who had served in World War II and been one of the men who raised the American flag in the iconic photo from Iwo Jima. His father never wanted to talk about his war experiences, and only after John Bradley's death did James learn that his father had received the Navy Cross for valor. This discovery led James Bradley to seek out veterans who'd fought at Iwo Jima and ask them about what happened, and to do some research on the other five men who appear in the photo. James Bradley found that much of what the public "knew" about the photo and the battle was erroneous. Most Americans thought the flag was raised at the end of the battle, after the U.S. Marines had defeated the Japaneses. The flag was really hoisted on the fifth day of a 35-day battle, by a contingent of Marines.

Shortly afterward, Navy Secretary James Forrestal requested that the flag be sent to Washington as a souvenir. When this flag was taken down, a new one had to be put up, by Marine Sergeant Mike Strank (Barry Pepper), Marine Corporal Harlon Block (Ben Walker), Marine Private First Class Ira Hayes (Adam Beach), Marine Private First Class Franklin Sousley (Joe Cross), Marine Private First Class Rene Gagnon (Jesse Bradford) and Navy Hospital Corpsman John "Doc" Bradley. While they did, photographer Joe Rosenthal took a snapshot. A few days later, Rosenthal's snapshot was published in newspapers all over the United States. The picture immediately become a symbol in a post Great Depression America, and the government decide to brings home the flag raisers, sent them on a tour to promote the war, and to raise funds, bringing hope to desolated people.

But only three surviving flag raisers, Rene Gagnon, John Bradley, and Ira Hayes, are whisked back to civilization to help raise funds for the war effort, the others were killed in action without being aware of the photo's widespread fame. However, the traumatized trio has difficulties to deal with the image build by their superiors, with the truth about the flags, and with sharing the heroism with their mates, when thousands of real heroes lie dead on Iwo Jima. The accolades for heroism heaped upon the three men are at odds with their own personal realizations, and that their own contributions to the fight are only symbolic and not deserving of the singling out they are experiencing. Each of the three must come to terms with the honors, exploitation, and grief that they face simply for being in a photograph.

Paul’s portayed Sgt. Henry “Hank” Hansen, firstly mistaken with Harlon Block in the pictures, Hank was in fact one of the men that rised the first, and real, flag. Hank died during the next days of the battle.

Clint Eastwood tried to option "Flags of Our Fathers" after the book by James Bradley and Ron Powers was published in May 2000. However, Steven Spielberg had already bought the rights that summer, and in early 2001, had assigned its adaptation to the screenwriter William Broyles Jr. Spielberg wasn't satisfied with the resulting screenplay and it laid dormant until he met with Eastwood at the Governor's Ball after the 2004 Oscar. After that, Eastwood took charge as the director with Spielberg as the producer.

The scene in which a sailor falls from a ship and is left in the water as the fleet steams toward Iwo Jima actually happened. The incident is described in of 'Iwo' by Richard Wheeler, himself a veteran of the fighting. Quote: 'According to Coast Guardsman Chet Hack of LST 763: "We got the man-overboard signal from the ship ahead of us. We turned to port to avoid hitting him and threw him a life preserver, but had orders not to stop. We could not hold up twenty-four ships for one man. Looking back, we could see him waving his arms, and it broke our hearts that we couldn't help him. We hoped that one of our destroyers or other small men-of-war that were cruising around to protect us would pick him up, but we never heard that they did."

Shot back-to-back with Letters from Iwo Jima (2006).

The Japanese government would not permit filming of combat scenes on Iwo Jima, so scenes were filmed in Iceland which also has black sand beaches due to volcanic activity.

The film was shipped to theaters under the code-name "Montana". Also, the first reel was shipped separately from the other seven to further prevent piracy.