Shinobi (忍び)
"ninja" is quite an interesting word, in fact the term is a native to Japanese (much like tsunami and other such words) and has the same meaning in English. It's literal meaning is "Those who endure", though it was used to describe the Japanese warriors who used ninjutsu to perform espionage and assassinations. The kanji spelling is 忍者 (ninja). Also, though the word mentioned previously can be used to address ninjas, it also has many other meanings like stealth and traveling incognito as it is the "masu" stem for the verb 忍ぶ (shinobu) which means "to conceal oneself" or "to hide". Thus as a noun, it's meaning must be drawn through context.
Ninja in Japanese is pronounced shinobi. (shin-o-bee)
Well, 'ninja' is a Japanese word, so you say it 'ninja'. You write it 忍者
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