The story of Secret Files: Tunguska begins with a puzzle. Nina Kalenkow's world is turned upside down when she learns that her father, the scientist Vladimir Kalenkow, has vanished without a trace. Since the polive can't (or won't) help, Nina decides to search for clues to her father's whereabouts on her own. On the way, she meets Max Gruber, one of her father's colleagues, who spontaneously offers the attractive young woman his help.

The trail leads Nina and Max to a mysterious disaster in the Tunguska region of Siberia in 1908, which Vladimir Kalenkow had been investigating. Does the disappearance of Nina's father have something to do with his previous expeditions to Siberia? The search for an answer leads the two heros from Berlin around the globe and to the Antartic, and it soon becomes clear that there are others who are also interested in Nina's father's secrets. After all, there's much more going on than the mere disappearance of an old man.