Set in early 17th-century Japan, shipwrecked English navigator John Blackthorne finds intrigue and culture shock in a feudal society that puts a premium on honor. A rival Lord sentences Blackthorne to death.

Blackthorne and Mariko begin a romance; Toronaga continues to build his army for a battle with Ishido. Anjin-san proves his mettle during an earthquake and is honored by Toranaga for bravery. Mariko's husband Buntaro, arrives in Anjiro.

Treachery, tragedy and turns of events occur. Toronaga becomes SHOGUN after the defeat of Lord Ishido. Mariko is killed in the final battle at Osaka Castle. Heartbroken, but resolute, Blackthorne begins construction of another ship.

After Lord Toronaga rescues Blackthorn from prison, he enlists him as his aide and names him, 'Anjin-san'. Mariko is directed to tutor Anjin-san in the language and customs of Japan.

Anjin-san's assimilation of Japanese ways is evident in his exemplary conduct. Toranaga decides to return the Erasmus to Anjin-san. Mariko tells Father Alvito of a plot to murder a Christian lord on the Council of Regents.