First of all, if you've made it to Master Ninja Mode, CONGRATS! The challenge of MN Mode is not much different than what was seen in Very Hard Mode (although there are a few unexpected surprises), so be prepared for a lot of frustration and pack a heavy lunch because you'll need the energy!
If you haven't unlocked Master Ninja Mode, there are two ways to do it: the Easy Way or the Hard Way. To unlock this mode the Easy Way, simply defeat Doku in Chapter 2 of Normal Mode to unlock Hard Mode, then defeat him in Hard Mode (same chapter) to unlock Very Hard Mode and then defeat Doku in Very Hard Mode (again, same chapter) to unlock Master Ninja Mode. By doing it this way, you'll forego having to complete the whole game on that particular difficulty.
If you CANNOT defeat Doku in Chapter 2 in either difficulty, then you'll have to unlock Master Ninja Mode the good ol' fashioned way by completing the game on each subsequent difficulty.
Once MN Mode is unlocked, be prepared for newer enemies and even more frustratingly cheap enemy tactics. Most (if not all) enemy attacks can kill you within a few hits and, since Ryu begins with an abnormally short Health bar, you'll need to learn to be super defensive as well as turn up your offense game.
These ninja enemies only appear in MN Mode and wear red-colored versions of the Black Spider Ninja outfits. While their attacks are the same as the Black Spider Ninja guys, the attacks they inflict have fire damage added. On Chapter 1, one combo from these guys will instantly result in a Game Over, so be prepared!
Just like the Red Spider Ninjas, these guys only appear on MN Mode. The only difference here is that these enemies now wear steel-armor mecha suits instead of their usual green-colored armor. Other than that, they are practically still the same enemy from Normal Mode.
When you first meet Marbus in Chapter 17, he will let you face off against the Clone rather than some lowly fiends (which makes it a total of FIVE Clone battles on MN Mode). For the battle, the Clone will have the Unlabored Flawlessness equipped, making him more dangerous as his health decreases during the fight.
The crab fiends will start appearing in Chapter 12 along with the Pincer fiends.
ARCHIVES ROOM NOTE: The Sorcerer fiend does NOT appear in this challenge.
GREAT BRIDGE NOTE: For this challenge, there are 40 of each enemy that appear. When the challenge begins, you'll fight 40 Ariochs, and then 40 Ogres, and then 40 Knightmares.
For Rachel's second challenge at the Military Gates, she'll face off against Pincer Fiends and Ogres (nearly similar to Very Hard Mode).
For Rachel's third challenge, the last 10 enemies will be Red Spider Ninjas.
That's all you need to know for Master Ninja Mode! Have fun and good luck with the Zarkhan Stadium Challenge! And if you really must know....you unlock absolutely NOTHING for beating MN Mode (except maybe bragging rights).