The land of Nippon is riven by civil war and the leaders of the different factions have a number of secret missions they need carried out. As master of one of the four great Ninja clans you must train your warriors so they are ready to carry out the missions offered. But beware, if you take too long one of your rival clans may undertake a mission before you and steal the rich reward offered for carrying it out.
In Shinobi: Way of the Ninja, you control a ninja clan and must perform different missions in order to obtain wealth and win the game. The missions you are called on to carry out are represented by three Mission cards that will tell you what you need to do (the task), where the mission is to be carried out (the location), and what problems may arise that will hinder you in the missions execution (complications). Each of these things requires one or more Skill cards from your hand to overcome. For example, if the mission required the use of unarmed combat you would need to play that Skill card in order to carry it out.
Once you have collected all of the Skill cards you need you may carry out a mission and reap the rewards for your clan. Unfortunately you will rarely have the right cards in your hand to perform a mission straight away. Instead you will need to store cards from your hand for future use by placing cards face-down from your hand into one of two dojos you control. Storing cards in this way represents you training the ninjas in your clan to perform a mission.
Keeping track of the cards placed in each dojo is challenging as you are not normally allowed to examine the cards once they are placed. You must use your powers of concentration and memory to remember which cards you have placed so that you can use them when you are ready to carry out a mission. Although this is difficult at first, you will find that your mental abilities quickly sharpen and that you will become increasingly skilled at the game. This is as it should be: being the master of a ninja clan requires great mental fortitude, and Shinobi: Way of the Ninja will test it to the utmost. However, if you get completely stuck, you can always visit the sensei who will (at a cost) allow you to examine the cards you have placed.
You receive a reward for completing each mission in the form of gold. The harder a mission the more gold you will receive, but the more cards you will need to play to carry the mission out. At the end of the game the player who has amassed the largest fortune wins.