Before starting, make sure the 6-button Genesis controller is plugged into controller port 1 while a regular controller is connected to the other port. At the main menu, highlight "Options." Then press and hold the Mode button on Controller 1, and press and hold D-pad Up and C on Controller 2. While these buttons on both controllers are still held down, go ahead and press the Start button on Controller 1 to enter the Options menu. If you performed the trick correctly, the Options menu should now read "Option" (without the "s" at the end) instead.
Now you can start a new game as normal. The A and B buttons are Block and Attack, respectively, while C is Jump. X allows you to use Ninjitsu magic, and the Y and Z buttons are used to throw Shurikens.
On the second section of the first level, at the first overhang section, there's a gap which you can jump up part way along, there's a Ninjitsu there.
On the first section of the third level, just before the boss section there's a box on the left wall. Jump on the box, do a crouching attack and then once you've picked up the Ninjitsu hop off the wall over the acid.
On the second section of the fourth level, right before the end there's a pipe you can jump up onto with a box containing a Ninjitsu.
On the second section of the sixth level right at the start there's a box just to the right of the exit containing a Ninjitsu.
On the last section of the final level just before the boss door there are 3 boxes, one containing a Ninjitsu.
There are 2 on the fifth level and at least another one on the sixth level but I forgot where those were. ^^;
If you find this section (with the falling rocks) to be tough then use the Ninjitsu of Fushin as that increases your jumping ability and will allow you to make the necessary jumps much easier.
In the second part of mission 3, if the lock on recticle locks onto you the screen will flash and you'll take damage. There is a way to avoid it. If you time your running dash attack (right/left twice then B) just right, there is a point where you're completely invincible, which is just as your sword is coming down. If you time this with the attack you will take no damage at all.
At the Options screen, set the number of starting shurikens to 0, then set sounds to "Shuriken". Highlight shurikens again and the 0 will change into an infinity symbol.
At the title screen, choose Options. In the Options menu, move down to the "S.E." command and use the B button to play these songs in order: "He Runs," "Japonesque," "Shinobi Walk," "Sakura," and "Getufu." Exit the Options screen and start your game. You are now invincible!