" The producers wish to acknowledge the extensive facilities accorded by the Air Ministry and by members of the Royal Air Force, also the valuable help received from Messrs. A.V. Roe & Co. Ltd. They wish also to record their appreciation of the approval willingly given to the telling of this story by all those represented in it and by the next of kin of the many members of 617 Squadron who, from this or later operations, did not return. " — Opening captions Spring 1942 : Aeronautical engineer Barnes Wallis is struggling to develop a means of attacking Germany's Ruhr Dams in the hope of crippling German heavy industry. Working for the Ministry of Aircraft Production, as well as his own job at Vickers, he works feverishly to make practical his theory of a bouncing bomb which would skip over the water to avoid protective torpedo nets. When it hit the dam, backspin would make it sink while retaining contact with the wall, making the explosion far more destructive. Wallis calculates that the aircraft will have to fly extremely low (150 feet (46 m)) to enable the bombs to skip over the water correctly, but when he takes his conclusions to the Ministry, he is told that lack of production capacity means they cannot go ahead with his proposals. Frustrated, Wallis secures an interview with Sir Arthur "Bomber" Harris, the head of RAF Bomber Command, who at first is reluctant to take the idea seriously. Eventually, however, he is convinced and takes the idea to the Prime Minister, who authorises the project. Bomber Command forms a special squadron of Lancaster bombers, 617 Squadron, to be commanded by Wing Commander Guy Gibson, and tasked to fly the mission. He recruits experienced crews, especially those with low-altitude flight experience. While they train for the mission, Wallis continues his development of the bomb but has problems, such as the bomb breaking apart upon hitting the water. This requires the drop altitude to be reduced to 60 feet (18 m). With only a few weeks to go, he is ultimately successful in fixing the problems as the deadline for the mission approaches. On 16 May 1943, the bombers attack the Ruhr Dams. Eight Lancasters and 56 men are lost, but the Möhne and Edersee dams are breached, causing catastrophic flooding. Wallis is deeply affected by the loss of the crewmen, but Gibson stresses the squadron knew the risks they were facing but they went in nevertheless. Wallis asks if Gibson will get some sleep; Gibson says that he has to write letters first to the dead airmens' next of kin.

Not long after the Pearl Harbor attack, United States Army Air Forces Lieutenant Colonel James Doolittle assembles two dozen North American B-25 Mitchell medium bombers with volunteer crews at Eglin Field, Florida, for a secret mission. Among them is Ted Lawson and his crew, co-pilot Lieutenant Dean Davenport, navigator Lieutenant Charles McClure, bombardier Lietuenant Bob Clever and gunner-mechanic Corporal David Thatcher. Given the opportunity to decline the mission, the crews opt to stay on, including Lawson whose pregnant wife Ellen joins him at Eglin Field. The crews are taught to take off from a runway only 500 feet long by a naval aviator from nearby Pensacola Naval Air Station. Lawson's plane acquires the nickname Ruptured Duck with nose art to match. Doolittle leads the group on a low-level flight at hedge-top height to Naval Air Station Alameda, California where their planes are loaded aboard the aircraft carrier USS Hornet. He informs the men their mission is to bomb Tokyo, Yokohama, Osaka, Kobe, and Nagoya. They will launch from the carrier 400 miles from Japan and after dropping their payloads continue to designated landing spots in parts of China controlled by Nationalist forces and regroup in Chungking. When an enemy surface vessel discovers the convoy, the crews are forced to take off twelve hours earlier than planned, to attack in broad daylight over Japan and land after nightfall in China. Doolittle leads the raid, dropping incendiary bombs to mark key targets for the others. The Ruptured Duck arrives over Tokyo to find some targets already burning, and attacks its targets as planned. Anti-aircraft fire bursts harmlessly around them, and confused enemy fighters ignore them. Ruptured Duck continues toward China and runs low on fuel approaching the coast in darkness and heavy rain. Lawson attempts a belly landing on the beach and crashes in the surf. With the exception of Thatcher, the entire crew is badly injured: Lawson's left leg is laid open to the bone, and McClure's shoulders are broken. Friendly Chinese soldiers help them, and the Americans face hardships and danger while being escorted through Japanese-held territory. In the absence of medical supplies, the injured men endure terrible pain, and Lawson's leg becomes infected. Delirious, he dreams of Ellen. A Red Cross banner hangs in the village of Xing Ming where Doctor Chung offers to take them to his father's hospital, 19 miles farther. He informs the men the Japanese have captured one of the other crews, and they hurry into the hills just before Japanese search parties arrive to burn the village down. No surgeon is at the elder Dr. Chung's hospital, but Lieutenant Smith's crew is on its way with Lieutenant "Doc" White, who volunteered as gunner. The Japanese approach, and the able-bodied Americans leave, except for Doc. He amputates Lawson's leg well above the knee, using the single dose of spinal anesthesia in their possession. It wears off too soon. Lawson passes out and dreams of Ellen. A chorus of Scouts singing " The Star-Spangled Banner ", in Mandarin, celebrates Lawson's first day out of bed. When the elder Dr. Chung gives Lawson an heirloom bracelet for his wife, Lawson is puzzled. He does not remember talking about her. When he totters on his crutches, he becomes distraught at the idea of Ellen seeing him without a leg. They hurry to Ch'ang Chou to rendezvous with an American plane that takes them home. General Doolittle visits Lawson in the hospital and tells him he has work for him to do. Lawson does not want to see Ellen until he obtains a prosthetic leg and learns to walk properly. Ellen arrives unannounced. Lawson forgets his missing leg and stands; he falls and Ellen rushes to him and the two embrace on the floor.

In 1942, Captain Yonoi is the commander of the POW camp in Lebak Sembada in Japanese-occupied Java. A strict adherent to the bushido code, his only connection to the prisoners are the empathetic Lieutenant-Colonel John Lawrence, the only inmate fluent in Japanese, and the abrasive spokesman Group Captain Hicksley, who repeatedly resists Yonoi's attempts to find weapons experts among the prisoners. Lawrence has befriended Sergeant Gengo Hara but remains at odds with the rest of the staff. Summoned to the military trial of the recently captured Major Jack Celliers, Yonoi is fascinated by his resilience and has him interned at the camp. Yonoi confides in Lawrence that he is haunted with shame due to his absence during the February 26 incident, believing he should have died alongside the rebels, implying his focus on honour stems from this. Sensing a kindred spirit in Celliers, Yonoi's fascination grows into a romantic obsession. When the inmates are made to fast as punishment for insubordination during the forced seppuku of a guard, Celliers is caught sneaking them food. They discover a smuggled radio during the subsequent investigation, forcing Celliers and Lawrence to accept blame. Yonoi's batman, realizing the hold Celliers has on him, attempts to kill Celliers in his sleep that night, but fails after he wakes up and escapes, freeing Lawrence too. Yonoi catches Celliers and challenges him to a duel in exchange for his freedom, but Celliers refuses; the batman returns and kills himself for his failure, urging Yonoi to kill Celliers before his feelings overpower him. At the funeral, Lawrence learns that he and Celliers will be executed for the radio to preserve order in the camp. Enraged, he trashes the funeral altar and is forced back into his cell. That night, Celliers reveals to Lawrence that as a teenager, he betrayed his younger brother, long bullied for his hunchback, by refusing to spare him a humiliating and traumatizing initiation ritual at their boarding school. He describes the lifelong shame it caused, paralleling Yonoi's predicament. The pair are released by a drunken Hara after another prisoner confesses to delivering the radio. As they leave, Hara calls out in English, "Merry Christmas, Lawrence!" Although angry at Hara for exceeding his authority, Yonoi only mildly reprimands him. Realizing that Yonoi wants to replace him with Celliers as spokesman, Hicksley confronts him and they argue about withholding information from each other. Enraged, Yonoi orders the whole camp to form up outside the barracks, including the sick bay's ailing patients, resulting in one's death. Hicksley, who refused to bring out the patients, is to be executed on the spot for his insubordination but before he can be killed, Celliers breaks rank and kisses Yonoi on each cheek. Caught between a desire for vindication and his feelings for Celliers, a distraught Yonoi collapses and is relieved of duty. The guards beat Celliers and drag him away. Yonoi's sterner replacement has Celliers buried in the sand up to his neck. Yonoi sneaks into his pen and cuts a lock from his hair, moments before his death. Four years later, Lawrence visits Hara, now a prisoner of the Allies. Hara has learned English and reveals he'll be executed the following day for war crimes. Expressing confusion over the harshness of his sentence given how commonplace his actions were among both sides of the war, he and Lawrence conclude that while the Allies officially won, morally "we are all wrong." They reminisce about Celliers and Yonoi, the latter of whom was reported to have been killed after the war, before bidding each other goodbye. As he is leaving, Hara calls out, "Merry Christmas, Mr. Lawrence!"