There were 49 schools of ninja in the country.
The most famous were Koka and Iga, in that time situated in different territories but closely related.
The Koka clan consisted of 53 families with one head family and many subordinates. This organization was called “Gunchu Sou” and the ninja families all acted together as a single group.
As for the Iga clan, there were a lot of schools like lone wolves The most famous among them was Hattori(Hattori Hanzo).
Koka and Iga were situated half way between Owari, Mikawa and the capital in Kyoto which was a strategically good position.
Films and novels about the Iga and Koga clans often feature one or the other as the villain,so It’s difficult to understand who was good and who was bad. But in reality,the two clans had a good relationship.
After the Honnoji Incident (The forced suicide of daimyo Oda Nobunaga by his samurai general Akechi Mitsuhide on June 21, 1582) the troops of Ieyasu became confused and disorganized and escaped from Osaka to a safe place (from Sakai to Mikawa) .
This all happened because of the collaboration between the Iga and Koka clans.
It they’d waited to,the Koka and Iga ninja working together could have killed Ieyasu, and if they did, the Tokugawa period would have ended at that, and history would have changed greatly.