The House of Gohda, where the Azuma Ninja Clan reside under the service of Lord Gohda, is on the brink of war with the neighboring country of Ogawara. As a new recruit in the Azuma Ninja Clan, the protagonist is sent to assassinate those who are assisting the country of Ogawara, including army generals and spies who have infiltrated the House of Gohda, as well as recover stolen items and rescue prisoners. In between thwarting the country of Ogawara's plans, the protagonist also receives missions in which he eliminates evil people such as abusive monks and greedy merchants.
There is no connection between Tenchu Z's plot and those in the previous games, nor are there any returning characters with the exceptions of Rikimaru and Lord Gohda.