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The Ninja is a Mercenary unit that can be sent from your Home City, or trained from the Saloon. These units are extremely effective against explorers and other mercenaries. Ninjas themselves are mercenaries, however, and are easily countered by spies or other ninjas.
The Ninja can also use Stealth Mode, which is detected by an Explorer or Town Center (or other units). There is a more powerful ninja, the Consulate Ninja, which costs export and is unique to the Japanese.