The third season of "Das Boot" follows the fate of an inexperienced submarine crew who are sent on a dangerous mission and find themselves in the sights of an obsessed Royal Navy commander. Under the leadership of Robert Ehrenberg (Franz Dinda), strong personal alliances form within the crew. Ehrenberg himself finds family ties that he thought were lost forever.

Meanwhile, in neutral Lisbon, where exiles, spies and criminals meet, Hagen Forster (Tom Wlaschiha) uncovers a deadly plot to steal looted war gold. His investigation also leads him to a man involved in a conspiracy that could change the course of the war for the better: Klaus Hoffmann (Rick Okon).