Tony's father Sam, abducted by aliens three years earlier, returns to earth and seeks out his wife and son, but Rachel has since been living with Joe and the reunion is awkward. Joe doesn't trust Sam, and Rachel can't quite decide what her feelings are for her two men. Sam is not the same as when he left, and he begins affecting Tony in frightening ways.
The body of one Cadogan West is found in an underground tunnel near Aldgate Station, with his skull smashed, and Holmes is puzzled by the interest his brother Mycroft is showing in the case. Mycroft explains that the top secret plans for a new submarine were in the dead man's pocket, but three of the ten pages were missing when the body was found. Mycroft, on behalf of the British Government, asks his brother to find the missing pages.