During that time, Hanzō, who was also a follower of the Ikkō-ikki, instead kept his loyalty to the Tokugawa clan and supported Ieyasu to fight the rebels.

According to the Kansei Chōshū Shokafu[a], Hattori Hanzō rendered meritorious service during the Battle of Mikatagahara and became commander of an Iga unit consisting of one hundred fifty men.

[16] In the middle of June 1582, after the Honnō-ji incident, Tokugawa Ieyasu escaped from Sakai to return into Mikawa, in order to prevent capture from Akechi Mitsuhide and his troops.

Ieyasu and his party, therefore, chose the shortest route back to the Mikawa Province by crossing through the Iga Province, which differed in many versions according to primary sources such as the records of Tokugawa Nikki or Mikawa Todai-Hon: Regardless of which theory is true, historians agreed that the trek ended at Kada (a mountain pass between Kameyama town and Iga).

[19] Portuguese missionary Luís Fróis had recorded in his work History of Japan, that during this journey, Tokugawa retainers such as Sakai Tadatsugu, Ii Naomasa, Honda Tadakatsu, Sakakibara Yasumasa, and many others[24]: 314–315 [18][25] fought their way out against the raids and harassments of ochimusha-gari outlaws during their march escorting Ieyasu, while sometimes also paying bribes of gold and silver to those which they could negotiate with.

[30][c] Hanzō participated in this conflict on the side of Tokugawa Ieyasu as he deployed his forces in various forts in the Kōfu basin against Ujinao, who camped his army in the area of present-day Hokuto city.

[33] At the same time, a Tokugawa army detachment from the Iga Province commanded by Hanzō invaded Saku District, where they were also aided by Shinano local samurai warriors from the Tsugane clan led by Ōbi Sukemitsu.

During this battle, Hanzo marched to Ise commanding 100 warriors of Iga and Kōka ninja as reinforcements from Matsugashima Castle.

By the time Ieyasu relocated to Kantō region, Hanzō was given an additional 8,000 koku worth of domain, along with the command of 30 yoriki officers and 200 civil officials.

[40][d] Hanzō's reputation as a samurai leader who commanded a 200-men strong unit of Iga warriors has grown to legendary proportions.

He was given the title Iwami no Kami (石見守)[43] and his Iga men would act as guards of Edo Castle, the headquarters of the government of united Japan.

The spear, originally 14 shaku (424 cm) long, 7.5 kg in weight, and given to him by Ieyasu, was donated to the temple by Hanzō as a votive offering, but was damaged during the bombing of Tokyo in 1945.

[48] Some of his other belongings are still in relatively good condition and can be viewed, but most other weapons, armour, and letters of commendation were lost due to a fire in Edo castle in 1606 that burned down his former quarters, the removal of his son from military command, and the chaos of the Siege of Osaka.

As a vassal of Tokugawa Ieyasu, Hanzō was more popularly known in modern era as archetypical ninja figure and is featured in many fictional works.

Hanzō only started to gain his acknowledgement as legendary ninja in fictional works in the 1950s in various mediums such as novels, manga, anime, Japanese television drama, movies, and theatre of Japan.