The Conquest of Iga, as recorded in Seishū Gunki
同年の冬、伊賀住人福地某が信長の味方になり伊賀追討の兵を要請した｡故に信長は信雄に伊賀を与え、各家臣に諸方から攻め込ませた｡伊勢､名張口は北畠中将信雄である。同じく馬野口は滝川左近将監一益である。長野口は長野上野介信包である。鹿伏兎口は神戸三七信孝である。甲賀山の口は多羅尾久右衛門尉が先陣を受けた｡下口は蒲生忠三郎氏郷である。大和笠置口は筒井順慶である。 伊賀の侍は防ぐ場所を失い其々城にこもった｡信雄は丸山城を落とした｡一益は富益城を落とし､富益氏は討ち死にして滅亡した｡また、具野尾城は落ちず、信孝は柘植城を攻め落とした｡氏郷は土山城を攻め数刻鉄砲合戦があった｡伊賀は大軍を受けてかなわず有るものは討たれ、あるものは降伏しみな信雄の支配下に入った｡故に信雄は丸山城を瀧川三郎兵衛尉に与え、柘植城を池尻平左衛門尉に与えた｡また、仁木友梅（前守護・義視）を取り立て平楽寺城に入れた｡
In the winter of the same year (1581), a certain Iga resident called Fukuchi became Nobunaga's ally, and requested for an army to launch a punitive expedition against Iga. Nobunaga granted Iga to Nobukatsu, and sent vassals to invade from all directions. From Ise, Nabari entrance, was the troops led by Lieutenant General Kitabatake Nobukatsu. At the same time, from Umano entrance, was the troops under Takigawa Sakon no Shōgen Kazumasu. From Nagano entrance, came Nagano Kōzuke no Suke Nobukane (Oda Nobukane). From the Kabuto entrance, Kanbe Sanshichi Nobutaka. The army coming from the entrance of Kōkayama was led by Lieutenant Tarao Kyūemon, while from the exit came Gamō Chūzaburō Ujisato. From the Yamato Kasagi entrance came the troops under Tsutsui Junkei. The samurai of Iga lost their defences, and holed themselves in their respective castles. Nobukatsu felled Maruyama Castle. Kazumasu felled Tomimasu Castle, and the entire Tomimasu clan were destroyed and killed. Gunō Castle did not fall, but Nobutaka attacked and conquered Tsuge Castle. Ujisato attaked Tsuchiyama Castle, and a gunfight lasted for a few hours there. Iga was no match for such a massive force, and some were defeated, while others surrendered themselves under Nobukatsu. After which, Nobukatsu granted Maruyama Castle to Lieutenant Takigawa Saburōbē and Tsuge Castle to Lieutenant Ikejiri Heizaemon. Also, he brought back Nikki Yūbai (the former shugo Nikki Yoshimi) and installed him in Heirakuji Castle.
(Seishū Gunki vol. 8)
In light of the recently released Assassin's Creed trailer, this really needed to be said:
Nobunaga does not invade Iga because he hated "ninjas"/shinobi. Nobunaga never participated in the Iga invasion and never directly led it.
Both are erroneous narratives that are constantly propagated both by Japanese and non-Japanese media, and this is just frustrating at this point. Some newer takes tried to "clean it up" by saying that Nobunaga invaded Iga as part of his nationwide conquest. That's a somewhat less wrong take on it, but if you put Nobunaga in direct command of the army, then it's still incorrect.
Both times the Oda forces attacked Iga, it was under the command of Nobunaga's son, Nobukatsu. After this final conquest, where Iga was thoroughly defeated in 1581, Nobunaga only came later to inspect the region. Everything had already been cleaned up, and the Shinchōkōki even recorded that there were lavish accommodations prepared for Nobunaga to stay in for the occasion.
Now going back to the narrative.
Seishū Gunki is somewhat less reliable than Shinchōkōki in various areas, but it's still a valuable material regardless. The are differences between this account and Shinchōkōki, though. For example, here Nobutaka was also listed as a participant. In the Shinchōkōki, Nobutaka was not listed as an officer that took part in the charge.
Another difference is that while Shinchōkōki corroborated Fukuchi surrendering himself to Nobunaga, it also mentioned that he was actually from Tsuge. Meaning that there was no need to attack and conquer Tsuge. Shinchōkōki also said that one of the Oda vassals went to Tsuge to protect it, and his name was listed as "Fuwa". In the above gunki narrative, this was the castle/region that Nobutaka attacked. It's likely that this part is in error in the gunki, and Nobutaka was not actually present here.
That aside, there has been various theories about why Nobukatsu attacked Iga, and there's an odd story of an Iga resident(s) who requested that the Oda invade his own homeland that was not explained in prior articles that I've seen. This request from the Iga folk themselves was what encouraged Nobunaga to grant permission for an official invasion of Iga, something that highly disapproved of 2 years prior.
This full text in the gunki provides an insight for the possible reason: It's possibly to restore the rightful shugo of Iga to power.
In the last part of the above text, a man named "Nikki Yoshimi" was referenced. The Nikki family was originally the official shugo (governors) of Iga. In a previous chapter of the gunki, it was mentioned that at some point they lost power, and the so-called council leadership of Iga became established.
If you've read the various floating narratives about how Iga is an "independent" society that is free from samurai rulership, this is how that supposedly came to be. The Nikki family were still there. They just got overrun by the people. If the above text is to be believed, the people who rebelled weren't peasants either. They were still considered of "samurai" class (they even own castles), just that they're perhaps of lower status (some texts would call them jizamurai).
If this narrative is actually accurate, then perhaps the men who came to the Oda for help were associates of the Nikki family. What they wanted was perhaps to the get rid of the "insurgents" who had rebelled and snatched power from the "rightful rulers".
So much for the mysticism of the secret "ninja" village and all, huh? It's just more of the typical power struggle between clans that are constantly happening in this time.
Incidentally, this situation is not entirely unique to Iga. A similar situation had occurred in Kaga almost a century prior, where the Ikkō from the Honganji affiliated temples there overthrew the shugo and ruled the land for a very very long time. Like in Iga, the shugo family were actually still there. They just effectively no longer had any power. The Ikkō rule remained until the Oda forces came and got rid of them as well.
Restoring the real governor into position was what I thought might have been the reason for this mess when I first heard of the Nikki clan last year (or two years ago?). It's just that I forgot to check this text. Interesting.