Short answers, pulled from the story.
The word ninja appears in written records as far back as the late 8th century within poems found in the Man'yōshū. A specific poem from that era reads Yorozu yo ni Kokoro ha tokete Waga seko ga Tsumishi te mitsutsu Shinobi kanetsumo.
Daisuke Togakure lost his lands after being defeated in a regional conflict around 1162 and traveled to mountains in southwest Honshu where he met Kain Doshi. They formulated guerilla tactics called ninjutsu which became counter-culture to the time, and his descendants founded the first ninja school known as Togakureryu.
Leading families established de facto independence from their shugo by the 1460s before the Kōka ikki persisted until 1574 when forced to become vassals of Oda Nobunaga. The Iga ikki continued until 1581 when Nobunaga invaded and wiped out organized clans, causing survivors to flee to mountains or arrive before Tokugawa Ieyasu who treated them well.
Rokkaku Yoshikata hired ninjas in 1558 to set fire to Sawayama Castle using deception techniques where a chūnin captain led forty-eight men into the castle stealing lanterns bearing enemy crests. This bakemono-jutsu allowed entry without fighting before setting fires to the structure, enabling capture of the fortress during chaotic rushes.
Between 1960 and 2010 artifacts dating to the Siege of Odawara were uncovered believed to be ninja weapons. Archaeologist Iwata Akihiro stated flat throwing stones stopped enemy movement while clay caltrops prevented castle invasions.