Though there are an abundance of primary documents attesting the history of the Iga ninjas, the majority were written decades later during the Tokugawa shogunate and were subject to distortion and exaggeration.

[8] A letter from Ichiborō a priest of Kongōbu-ji to Futami Mitzuzōin, dated September 12, 1580, describes a counter-attack by the Iga ikki against an ally of Oda Nobunaga, Sakaibe Hyōbudaiyū.

[9] Amagoisan rōjō okite kaki — Written Regulations for the Siege of Amagoison, a fifth and undated document, describes events from the Tenshō Iga War.

While Kawakami Jinichi, a historian at Mie University, dates the document to 1579, because Oda Nobukatsu in that year invaded from Ise Province while the work mentions the invasion of Iga coming from Kōka, historian Stephen Turnbull believes that Amagoisan describes the second invasion by Oda Nobunaga in 1581, specifically the force led by Gamō Hidesato along Tamataki route from Kōka.

[20] The militant mountain-monks, yama-bushi, were also likely an influence as even the bandits in the area wore yellow scarfs that seem to have been copies of those worn by the mountain monks.

[24] However, in 2017, Turnbull questions the existence of such a market at all, contending that, contrary to the mercenary narrative, political self-interest, including continued survival, could also have equally motivated the activities of Iga units in these provinces.

[25] The usages of the term shinobi, specifically shinobi-mono, later known as ninjas, appearing in the late 1580s and early 1600s, referred to the soldiers from Iga and Kōka.

[28] Records of their military unit, Iga-shū, appear as early as June 1470, when they assisted the Hatakeyama clan in an attack in the fields outside the Negoro-ji in Wakayama.

[28][30][29] In 1487, the ninja from Iga and Kōka gained significant fame due to their actions at Magari, which is part of present-day Rittō, Shiga.

The illness which prematurely killed Yoshihisa may have been at least hastened by, if not caused by wounds suffered during, the guerilla tactics and night attacks by the Iga and Kōka units.

[32] On December 15, 1541, the shogun in Kyoto sent a letter to Iga's governor requesting that the province assist Tsutsui Junshō in his siege of Kasagi Castle.

[33] In the morning of December 23, 1541, 70–80 ninja agents from Iga and Kōka infiltrated the castle, set fire to the settlement, and were said to have captured the first and second baileys.

[36] The historian and travel writer John Man, on the other hand, takes the account at face value and cites this as an example of the fame of the ninjas and of them offering their services for hire.

[11] In 1560, a highly influential leader within the confederacy, Shimotsuge no Kizaru, attacked Tōichi Castle (present-day Kashihara, Nara), which was commanded by Hashio Shōjirō Tōkatsu.

[41] Jizamurai from Iga and Kōka assisted Jōtei and his sons in raids against Nobunaga, including setting fire to the village of Heso and the southern approaches of Moriyama.

[41] On July 6, 1570, these alliance forces were moving down along the Yasugawa river when an army led by Shibata Katsuie and Sakuma Morimasa, generals for Nobunaga, intercepted them at the village of Ochikubo.

[42] Stephen Turnbull estimates that 780 casualties must have been enormous for Iga and Kōka, since their armies likely were not very large, and indeed Shinchō Kōki makes no reference to that alliance for the next three years.

[43] A later record states that in 1573 some Iga-shū supported Shibata Katsuie and other retainers of Nobunaga in defeating the Azai clan in the Siege of Odani Castle.

[49] The historian Stephen Turnbull summarized the defeat as "one of the greatest triumphs of unconventional warfare over traditional samurai tactics in the whole of Japanese history.

[65] The poet Matsuo Bashō was born in Ueno to a powerful ninja family and was trained in ninjutsu before he left to study haiku.

[27] In times of military crisis, the shugo would sometimes temporarily exercise his powers in nearby Yamato Province, which normally was under autonomous rule by Kōfuku-ji via the authority of the Fujiwara clan.

[70] Around the year 1560, a constitutional document was drawn up for Iga outlining principles of self-defense and participation of villages based on voluntary association.

[38] Eleven points were laid out in the constitution:[71] To coordinate the Iga–Kōka alliance, the respective confederacies frequently held "field meetings" along their border to discuss issues of governance and cooperation.

[52][72] This co-operation within and between Iga and Kōka was in tension with constant petty feuds in each of the regions that helped contribute to the development of the leagues in the first place.

[13] Even though the sō was embedded within a feudal hierarchy, it had democratic tendencies and the possibility of social mobility through promotion meant that class differences could be overcome.

[76] Conversely, Eiko Ikegami states that 10 magistrates oversaw the collective, with important matters discussed at meetings with the entire membership of the ikki,[68] while a 2017 book published by Mie University argues that the bands of clans overseeing different portions of territory were overseen by 12 leaders known as hyojo-shu.

[13] The Russian economist Vladimir V. Maltsev hypothesizes that the formation of a private and voluntary government allowed Iga the stability to reap profits from its mercenary market while remaining effectively stateless.

[78] In most of Japan after the Onin War, the loss of centralized power and the ensuing banditry, peasant uprisings, and feuds between and predatory taxation and raids by local daimyō resulted in insecure property rights, thin markets, and greatly weakened provision of public goods.

[75] Okuse Heishichirō, the writer who in the mid-20th century greatly contributed to the development of ninja myth, outlined a three-tiered social structure in Iga.

[23] Some of the most famous ninja commanders came from these families, namely the legendary figures Momochi Sandayu, Fujibayashi Nagato no Kami, and Hattori Hanzō, all three of whom Okuse labeled jōnin.