In 1944 in the USA, nuclear physicist Alvah Jesper, a handsome bachelor who is working on the Manhattan Project to build an American nuclear bomb, is recruited into the Office of Strategic Services. His mission is to make contact with a Hungarian nuclear physicist, Katerin Lodor, who has been working on the German project to make a nuclear bomb and has escaped into neutral Switzerland. Flown into Switzerland, Alvah finds it full of German agents who, after he manages one brief conversation with Katerin, abduct her. By befriending and then blackmailing an attractive female agent, he discovers where Katerin is being held, but an OSS raid on the building fails and she is shot dead. In the conversation, she had said that the Germans wanted her to work with an Italian nuclear physicist named Polda. The OSS land Alvah in Italy from a British submarine and he is hidden by an attractive member of the Resistance, Gina. He manages to obtain a brief conversation with Polda, who agrees to work with the Americans only if the OSS first free his daughter Maria, who is being held by the Germans. The OSS raid on the building is successful and in an isolated safe house they deliver Maria to her father. He is horrified, because it is not his daughter but a German agent, who says the house is surrounded by German troops. In the ensuing gun battle, Alvah and Gina smuggle Polda out through the cellar and struggle across country to a rendezvous with a British aircraft which will fly them out. Polda and Alvah board it safely, but Gina says she must stay behind to free her country from the Germans and begs Alvah to come back for her when the war is over.
As planned by Lang, the film had a different ending. Jesper leads a group of American paratroopers into Germany to discover the remains of an underground factory, the bodies of dead concentration camp workers, and evidence the factory was working on nuclear weapons. Jesper remarks that the factory may have been relocated to Spain or Argentina and launched a diatribe saying: "This is the Year One of the Atomic Age and God help us if we think we can keep this secret from the World!" Producer Milton Sperling, who had frequently quarreled with Lang on the set, thought the final scene ridiculous, since the audience knew the Germans had no nuclear capacity. Screenplay writers Lardner and Maltz became two of the Hollywood Ten, accused of adding communist dogma to movie scripts such as this one. Writing a script saying the US could not keep nuclear secrets from the USSR, such as in this film, was just one of many accusations against the Ten.
Radio show
A 1950 NBCradio show of the same title based on Ford and MacBain's book lasted 26 episodes. Cloak and Dagger began with actor Raymond Edward Johnson asking "Are you willing to undertake a dangerous mission for the United States knowing in advance you may never return alive?"
