Frank Griffin Jr., the grandson of the original Invisible Man, runs a Manhattan print shop under the assumed name Frank Raymond (Jon Hall). One evening, four armed men burst into the shop and reveal that they are Axis agents who know his true identity. Among them, Conrad Stauffer (Cedric Hardwicke), a lieutenant general of the SS, and Baron Ikito (Peter Lorre), a Japanese operative, demand the invisibility formula and threaten to amputate his fingers if he won’t disclose it. Griffin manages a narrow escape with the formula and, after Pearl Harbor, agrees to limited cooperation with U.S. officials on one condition: the serum can only be used on himself.
During a covert mission, Griffin injects himself with the serum and becomes invisible as he parachutes behind German lines, landing and quickly stripping off his clothing in the shock and confusion of pursuing troops. He evades capture and seeks out Arnold Schmidt ([Albert Bassermann]), an old coffin-maker who knows the next step: Griffin must obtain a list of German and Japanese spies within the United States that is in Stauffer’s possession. Graced with a new ally, Griffin receives crucial help from Maria Sorenson ([Ilona Massey]), a German espionage agent who is entangled with both Stauffer and his second-in-command, the scheming Karl Heiser (J. Edward Bromberg). During a private dinner intended for interrogation, Sorenson tries to press Heiser for information; Griffin, invisible, pranks the table, leaving Heiser furious and Sorenson effectively under house arrest. To prove his disguise to Sorenson, Griffin reappears in a robe and smears facial cream on his features, and the pair’s mutual attraction deepens.
Conrad Stauffer returns from his efforts in the United States and juggles shifting loyalties with Maria Sorenson and Karl Heiser, while Baron Ikito stays close at the Japanese embassy. When Heiser’s dinner with Sorenson ends badly, Stauffer arrests Heiser and sets a trap for Griffin, whom he suspects has made contact with Sorenson. Despite walking into the trap, Griffin still manages to seize the spy list and ignite a fire to cover his escape. He delivers the list to Schmidt so it can be transmitted to England, while Stauffer tries to hide the loss from Ikito, who has been staying at the Japanese embassy. The two men acknowledge privately that German-Japanese cooperation is fragile and built on tenuous trust.
Griffin then infiltrates a German prison to pressure Heiser for information about a planned German attack on New York. In exchange for more intelligence, Heiser helps Griffin escape, and Griffin returns with Heiser to Schmidt, who has meanwhile been arrested and tortured by Stauffer. Back at the shop, Griffin confronts Sorenson, whom he suspects of betrayal, and is captured with a net by Ikito’s men. Heiser, covertly, calls in Ikito’s activities to Stauffer in an effort to salvage his own position. Griffin and Sorenson are taken to the Japanese embassy but escape amid the chaos when Stauffer’s men arrive.
Ikito kills Stauffer and then performs seppuku, witnessed by Heiser, who takes command too late to stop Griffin and Sorenson from escaping. The pair steal a bomber bound for New York and, while in flight, shoot down other German planes on the ground as they head toward England. Stauffer’s loyal men catch up with Heiser and shoot him, and Griffin loses consciousness just before radio contact can be made. England’s air defense eventually shoots down their craft, but Sorenson parachutes them to safety. In a hospital, Griffin has recovered and continues to wear facial cream so he can remain visible. Sorenson arrives with Griffin’s American handler, who confirms that she has been an Allied double-agent all along. Sorenson is left alone with Griffin, who reveals that he remains visible beneath the cream, and they share a kiss. Sorenson accepts the challenge of discovering how Griffin regained his visibility, ready to continue the fight on the side of the Allies.
