Everything begun in 1603 during the Tokugawa shogunate, the Supreme Commander of all the ninja villages throught Japan, Hattori Hanzo got killed in 1596 but his death was kept a secret for years until the inormation leaked out and in a few years all the villages knew about it.
Hattori Hanzo was in charge of keeping the peace between the villages that were in constant war. After his death most remained in eace but two resumed their war, this two villages are the Iga and the Kouga, even today in 2017 they live and fight as they used to in the 1600, of course, they have contact with modern society.