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Ninja Timeline
Taken from the Densho Scrolls

Ninja rendered distinguished services in restoring peace to the province of Yamato (present-day Osaka) for Emperor Jinmu, and also in suppressing barbarians know as the Ainu.
Ninja raised an army in loyalty to Southern Court of Yoshino (1331-33 A.D.) They joined armies of Nawa, Kusunoki, Kitabatake (1334-35 A.D.)
Ninja put the Ashikaga Army into confusion (1487-88 A.D.)
They joined the army of Sekita and chased the large army of Hosokawa Takakuni under the Ashikaga shogun's command (1504-20 A.D.)
In those days, the ninja had no specific schools like Koga or Iga ryu, and were distinguished by the name of the places where they lived.  Ninja living in both Koga and Iga provinces were royalists.  However, when Ashikaga Yoshitane dispatched his troops to the Omi district to subdue Ashikaga Yoshizumi, Koga ninja took sides with Yoshitane while Iga ninja would not, which caused discord between the ninja of Koga and Iga.
Iga ninja cooperated with the Royalists army (1854-59), and joined a squad of the court patrolmen and troubled the Shinsengumi or bodyguard of the Tokugawa government organized in the closing days of the shogunate.
In 1863, some ninja joined Tenchugumi or a group of extremists headed by Yoshimura Torataro, Fujimoto Tesseki, and others who tried to overthrow the Tokugawa shogunate.  They rose in arms to no effect and many were killed.
Ninja distinguished themselves in the field of battle against the Tokugawa government. In the battle of Toba Fushimi, which as fought between royalists and the loyalists of the Tokugawa shogunate just after the decree of the Restoration of Royal Rule in 1886, ninja joined the Royalists party, distinguishing themselves in it.