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The main character is Karl Fairburne, an OSS officer who is inserted into Berlin in 1945, during the final days of World War II. It references Operation Paperclip and its predecessor Operation Overcast, the plan by the USA to recruit the scientists of Nazi Germany. Fairburne comes up against both Nazi and Soviet opponents as he seeks to kill or capture key scientists involved in the V-2 rocket program.

The campaign begins with a tutorial mission were the player must assassinate German Major-General Hans von Eisenberg who is attempting to defect to the Soviets. The next mission is a slightly altered version of the demo, where the player is sent to kill Dr. Gunther Kreidl, a Nazi scientist and search escape with his documents. Next, Fairburne infiltrates a V2 rocket production facility in search of another scientist, Dr. Schwaiger, who is willing to defect to the United States, but Fairburne is discovered and must fight his way out of the facility. Fairburne decides to steal a cache of explosives and destroy a bridge to distract the Soviets and Germans while he slips behind them and rescues Schwaiger.

The plan works and Fairburne heads off to a place called Opernplatz, where he finds Schwaiger and is forced to hold off waves of Soviet troops who have discovered their position. Schwaiger is shot in the process, and before he dies, he says "tabun". Fairburne, clueless, goes to find Dr. Müller, whom he assassinates from his command tower. With no location of V2 launching site, he goes to a Soviet HQ, where he finds that tabun is a nerve gas inside the V2 rockets that are about to launch on London. With only information that location is somewhere outside Berlin, Fairburne goes to Berlin's office of Dr. Wolff's, the mastermind behind the project, to find clues. The office has been already destroyed, but Fairburne finds a ripped notebook and he finds that Wolff is about to escape from an airfield. Fairburne arrives at the ministry building with a map that is thrown in a fireplace, he barely puts out the fire and the location of the V2 rockets are found. He sets out to destroy them, which he successfully does.

With only Wolff left, Fairburne goes back to the Brandenburg Gate, where he had assassinated von Eisenberg few days earlier. Fairburne climbs on top of the Gate and, as Wolff is about to escape in a car, he shoots, making the car run off the road and crash, killing Wolff instantly. Fairburne remarks that WWII is over but the Cold War begins, of which he was the first American soldier.