Plot Synopsis (contains spoilers)
Lord Goda and the neighboring country of Ogawara are on the brink of war. Various trades and political engrossments have increased tension between the two and the Azuma Ninja Clan, now well established and headed by Rikimaru, are to defend the land of Gohda. However, Ogawara is and his armies, along with his personal ninja Shigi, are strong and the Azuma Clan needs your help to take down the rival country. According to the cut scenes, you and your partner left your old lives behind without looking back, in order to become ninjas under Rikimaru’s tutelage. Whether you are male or female does not impact the story.
As you eliminate spies, gather information, and assassinate those in cooperation with Ogawara, Shigi begins to interfere with your missions. In your first meeting with Shigi he will kill your target before you do so, and provide a boss battle for that level. He is a master at ninjutsu and the art of the sword, as well as stealth and assassination techniques as seen in other cut scenes and during the fight. At some point in the story Shigi ambushes you and your partner at the end of a mission and your partner has disappeared. Shigi captures and tortures your partner until you come to rescue him/her, but to no avail as the injuries were to grave and your partner dies in your arms. The story progresses as you complete your missions getting closer and closer to your goal, Ogawara himself. Once you beat the last level it appears that Shigi actually assists your assassination of Ogawara for reasons unknown, and he seems to possess some sort of knowledge of Rikimaru. The story in Tenchu Z takes backseat really, as the missions each have their own side story that adds to the main plot. Going into each one would be repetitive and pointless as they usually don’t actually affect the story directly, although there are some missions specifically for advancement of the story.