Short answers, pulled from the story.
Ninja served as spies, scouts, saboteurs, surprise attackers, and agitators in feudal Japan. Espionage was their chief role; they gathered information on enemy terrain, building specifications, and passwords through the use of disguise. Arson was their primary form of sabotage, directed at castles and military camps.
Ninja originated among the jizamurai, peasant-warriors of Iga Province (now Mie Prefecture) and the adjacent Koka District. By the 1460s, the leading families in these regions had established de facto independence and organized themselves into ikki, or leagues, selling their services as mercenaries and spies. Professional ninja were actively hired by daimyo between 1485 and 1581.
Shinobi and ninja refer to the same agents but come from different readings of the same two kanji. Shinobi is the native Japanese reading and was almost always used in historical documents. Ninja is the on'yomi reading, influenced by Early Middle Chinese, and was rarely the term used in practice.
The last documented use of ninja in open warfare was during the Shimabara Rebellion of 1637-1638. Shogun Tokugawa Iemitsu deployed Koga ninja against Christian rebels at Hara Castle in Hizen Province. The Ukai diary and the Amakusa Gunki provide detailed accounts of their reconnaissance and infiltration missions during that siege.
The black ninja costume was invented in Edo-period kabuki theatre, not on any battlefield. Playwrights dressed ninja characters in the same black outfits worn by kuroko, the stagehands who were dressed to be ignored by audiences. The theatrical image of the stealthy, black-clad ninja spread from stage to popular fiction and eventually to modern media.
The Bansenshukai, compiled in 1676, is the most notable of the shinobi manuals written in the 17th and 18th centuries. It draws heavily on Chinese military philosophy and describes forty-eight types of ninjutsu. Its original source text, the Kanrinseiyo, was discovered in a warehouse of Kazuraki Shrine in Koka city on the 19th of June 2022 in a handwritten reproduction made in 1748.