information:classification, linguistic:paraphrasing, linguistic:translation
Further activities after 1582

In an undisclosed time, a ninja named Hachisuka Tenzō was sent by Nobunaga to assassinate daimyō Takeda Shingen, although it ended in failure. There is a record that there is an assassination attempt were on Toyotomi Hideyoshi, although it was thwarted. A ninja named Kirigakure Saizō (possibly Kirigakure Shikaemon) attempted to assassinate Hideyoshi with a spear, but was unsuccessful, as his attempt was foiled by a ninja worked under the command of Hideyoshi who smoked his place. However, the reliability of this story was considered fictional publications as it was the same publisher which depicted Saizō as one of the legendary Sanada Ten Braves.

In 1600, during the Sekigahara Campaign after the Eastern Army's victory at Sekigahara, the Iga acted as guards for the inner compounds of Edo Castle, while the Kōka acted as a police force and assisted in guarding the outer gate. It was said that at one occasion, a group of Mogami clan 's ninja infiltrated the camp of Naoe Kanetsugu, stealing his battle standard, which later hoisted on the Hasedō Castle's gate, demoralized the Uesugi troops greatly in effect.

In 1603, a group of ninja from Iga clan led by Miura Yo'emon were assigned under the command of Red Demon brigades of Ii Naomasa, the daimyo of Hikone under Tokugawa shogunate.

In 1608, a daimyo named Tōdō Takatora was assigned by Ieyasu to control of Tsu, a newly established domain which covered portions of Iga and Ise Province. The domain at first worth of to the 220,000, then grow further in productivity to the total revenue of 320,000 koku under Takatora governance. It was reported that Tōdō Takatora employs the Iga-ryū Ninjas. Aside from Ninjas, he also employs local clans of Iga province as "Musokunin", which is a class of part time Samurai who has been allowed to retain their clan name but does not own any land or Han. The Musokunin also worked as farmer during peace, while they are obliged to take arms in the time of war.

In 1614, The Iga province warriors saw action during the siege of Osaka. Takatora brought the Musokunin auxiliaries from Iga province to besiege the Osaka castle during the winter phase. Meanwhile the ninja units of Iga province were deployed under several commanders such as Hattori Hanzō, and Yamaoka Kagetsuge, and Ii Naotora, heir of Naomasa who also given control of Ii clan's Red Demons ninja squad after Naomasa died. Later in 1615, during the summer phase of Osaka siege, The Ii clan Red Demons ninjas led by Miura Yo'emon, Shimotani Sanzo, Okuda Kasa'emon, and Saga Kita'emon saw action once again during the Battle of Tennōji, as they were reportedly fought together with the Tokugawa regular army storming on the south gate of Osaka castle. In 1614, the initial "winter campaign" at the Siege of Osaka saw the ninja in use once again. Miura Yoemon, a ninja in Tokugawa's service, recruited agents from Iga province, and sent 10 of his members into Osaka Castle in an effort to spread rumors and misinformation to weaken the enemy forces internally. Later On the Osaka battles, these hired ninja fought alongside regular troops at the Battle of Tennōji.

A final but detailed record of ninja employed in open warfare occurred during the Shimabara Rebellion (1637–1638). The Kōga ninja were recruited by shōgun Tokugawa Iemitsu against Christian rebels led by Amakusa Shirō, who made a final stand at Hara Castle, in Hizen Province. A diary kept by a member of the Matsudaira clan, the Amakusa Gunki, relates: "Men from Kōga in Ōmi Province who concealed their appearance would steal up to the castle every night and go inside as they pleased."

The Ukai diary, written by a descendant of Ukai Kanemon, has several entries describing the reconnaissance actions taken by the Kōga.

They were ordered to reconnoitre the plan of construction of Hara Castle, and surveyed the distance from the defensive moat to the ni-no-maru (second bailey), the depth of the moat, the conditions of roads, the height of the wall, and the shape of the loopholes.

Suspecting that the castle's supplies might be running low, the siege commander Matsudaira Nobutsuna ordered a raid on the castle's provisions. Here, the Kōga captured bags of enemy provisions, and infiltrated the castle by night, obtaining secret passwords. Days later, Nobutsuna ordered an intelligence gathering mission to determine the castle's supplies. Several Kōga ninja—some apparently descended from those involved in the 1562 assault on an Imagawa clan castle—volunteered despite being warned that chances of survival were slim. A volley of shots was fired into the sky, causing the defenders to extinguish the castle lights in preparation. Under the cloak of darkness, ninja disguised as defenders infiltrated the castle, capturing a banner of the Christian cross. The Ukai diary writes,

We dispersed spies who were prepared to die inside Hara castle.... those who went on the reconnaissance in force captured an enemy flag; both Arakawa Shichirobei and Mochizuki Yo'emon met extreme resistance and suffered from their serious wounds for 40 days.

As the siege went on, the extreme shortage of food later reduced the defenders to eating moss and grass. This desperation would mount to futile charges by the rebels, where they were eventually defeated by the shogunate army. The Kōga would later take part in conquering the castle:

More and more general raids were begun, the Kōga ninja band under the direct control of Matsudaira Nobutsuna captured the ni-no-maru and the san-no-maru (outer bailey)...

With the fall of Hara Castle, the Shimabara Rebellion came to an end, and Christianity in Japan was forced underground. These written accounts are the last mention of ninja in war. After the Shimabara Rebellion, there were almost no major wars or battles until the bakumatsu era. To earn a living, ninja had to be employed by the governments of their Han (domain), or change their profession. Many lords still hired ninja, not for battle but as bodyguards or spies. Their duties included spying on other domains, guarding the daimyō, and fire patrol. A few domains like Tsu, Hirosaki and Saga continued to employ their own ninja into the bakumatsu era, although their precise numbers are unknown.

Many former ninja were employed as security guards by the Tokugawa shogunate, though the role of espionage was transferred to newly created organizations like the onmitsu and the oniwaban. Others used their ninjutsu knowledge to become doctors, medicine sellers, merchants, martial artists, and fireworks manufacturers. Some unemployed ninja were reduced to banditry, such as Fūma Kotarō and Ishikawa Goemon.