Allow the following events to occur during story mode to unlock the corresponding special mission:
Mission 2.1 (Departures): Do not kill all the enemies in Mission 1.
Mission 2.2 (Determination Kill): Kill all the enemies in Mission 1.
Mission 6.1 (The Blind Masseuse): Allow at least one enemy to spot you in Mission 5.
Mission 6.2 (What Lurks in the Shadow): Do not get spotted in Mission 5.
Mission 7.1 (A Sister's Promise): Get the map in Mission 6.
Mission 7.2 (For Whom the Bell Tolls): Leave the map in Mission 6.
Mission 10.1 (Flames of Passion): Allow the samurai to live at the beginning of Mission 9.
Mission 10.2 (Flames of Sorrow): Kill all three enemies at the start of Mission 9.
Mission 12.1 (Tenchu Kurenai): Kill Ranzo.
Mission 12.2 (Tenchu Kurenai): Allow Ranzo to escape.