It's March 1943 and mathematician Tom Jericho (DOUGRAY SCOTT) has returned to Station X at Bletchley Park, the center of British code-breaking operations against the Nazis. Although Jericho is considered a brilliant code breaker, his previous nervous breakdown - the result of either too much work or his brief but failed romance with Claire Romilly (SAFFRON BURROWS) - has left certain other code breakers and officials there, including Skynner (ROBERT PUGH), doubtful of how much he'll be able to contribute to solving the latest crisis.
It seems that the Nazi U-boats have changed the code generated by their enigma machines to communicate with each other and the German command. The danger is that a large convoy of Allied merchant ships is headed across the North Atlantic and reports have it that several packs of German subs are hunting them down.
Accordingly, it's up to Tom and other code breakers such as Baxter (RICHARD LEAF) and Puck (NIKOKAJ COSTER WALDAU), who are working under the supervision of naval liaison Cave (MATTHEW MacFAYDEN), to crack the code before the Germans sink any ships. Adding to the mix is the presence of Wigram (JEREMY NORTHAM), an intelligence officer who believes a spy may have been and/or currently be in their midst.
Yet, Tom has his own mystery to solve and that's the whereabouts of Claire whose roommate, Hester Wallace (KATE WINSLET), has reported her missing. As Tom fondly recalls his brief, happy time with his former lover, he and Hester try to solve her disappearance as well as her possible involvement with the code-breaking operation, all while hoping to decipher the Nazis' code before lives are lost at sea.