In May 1941, commandos Paul Toledo and Natasha Nikochevski capture an Enigma machine and its codebook in a German submarine base at La Pallice in La Rochelle, France. While Natasha leaves the base, Toledo is ordered to stay behind with the Enigma to assist the other commandos (Jack O'Hara, Thomas Hancock, James Blackwood & René Duchamp) when they arrive at daybreak to rescue the crew of a Royal Navy submarine, the E-423, sheltered and under heavy guard in a submarine pen. They destroy the base's anti-aircraft guns and torpedo warehouse before escaping in the submarine.

While in the North Sea, the Royal Navy submarine is caught and forced to surface in the frigid waters after being depth charged by a German destroyer. The enigma machine is confiscated and the entire crew captured with the exception of Blackwood and Hancock, both of whom evaded capture. After rescuing the crew, the commandos proceed to recover the Enigma and disable the destroyer's main guns and boiler room. Under orders that the Enigma be hastily brought to England, O'Hara and Duchamp takeoff in a Fieseler Fi 156, while the rest escape in the submarine.

A year passes and the commandos are deployed to the Pacific Theatre. In Burma, they rescue a spiritual leader and assassinate a Japanese tyrant with the help of Gurkhas. On 17 June 1942, the commandos are sent to northern Thailand, where they rescue a Colonel Guinness, who in turn helps them destroy the bridge over the River Kwai by revealing its structural weakness. The bridge is blown up just as a train of the Imperial Japanese Army high command crosses it, plummeting into the river.

In July 1942, the commandos land on the strongly fortified Savo Island to disable the large artillery guns, before Operation Watchtower can commence. While on the island, they are assisted by a castaway named Wilson. After destroying the artillery and rescuing a downed American pilot, he returns the favour by piloting a Kawanishi H8K to help them escape the island, but not before telling them of a gold monkey statue which is symbolic to the Japanese. O'Hara steals it as a souvenir.

In Spring of 1944, the commandos are sent to Haiphong, Indochina, destroying the port's fuel depots and infiltrating the Japanese aircraft carrier Shinano. While out at sea, the commandos sabotage the rudder of every A6M Zero and report the carrier's position before escaping in two intact Zeroes. The Shinano is then bombed by American Vought F4U Corsairs.

Following their tour of duty in the Pacific, the commandos are recalled to the Western Front for the Normandy invasion. During the battle of Cherbourg, they rescue a wounded Private Smith, and with the help of American soldiers, successfully defend the town from waves of German infantry and Panzer III tanks. A few months later, Toledo is captured and taken to Colditz Castle where he is to be executed. The commandos save him and they help the prisoners of war housed there escape by disguising them in German uniform. While the prisoners escape, the commandos acquire top secret documents from three high-ranking German officers, revealing plans to devastate Paris with planted explosives before it is liberated.

In August 1944, the entire commando corps arrive in Paris and thwart plans to destroy much of the city, before leaving in an airship from top of the Eiffel Tower