Short answers, pulled from the story.
The ninja emerged as a distinct class in the 15th century, although espionage in Japan dates back to the 6th century. Prince Shotoku employed a spy named Otomono Sahito around the year 574, but the figure known as the ninja did not exist until later. The true lineage began in 1162 when Daisuke Togakure formulated ninjutsu with Kain Doshi.
The Iga and Kōga clans were jizamurai families who carved out de facto independence in the remote mountains of Iga Province and the adjacent Kōka District. By the 1460s, these families established their own leagues known as ikki, which functioned as self-defense organizations that sold their services as mercenaries and spies to the highest bidder. The alliance between Iga and Kōka was formalized in a constitutional document around 1560.
The Iga ikki held out until 1581 when Oda Nobunaga invaded and wiped out the organized clans. The survivors fled to the mountains of Kii or found refuge with Tokugawa Ieyasu, where they were well treated. Hattori Hanzō, a former Iga clan member, later served as Tokugawa's bodyguards, bridging the gap between the outlawed mountain clans and the new shogunate.
Arson was the primary form of sabotage practiced by the ninja, targeting castles and camps with ruthless efficiency. In 1558, Rokkaku Yoshikata employed a team of ninjas to set fire to Sawayama Castle using a technique dubbed bakemono-jutsu. A chūnin captain led a force of 48 ninja into the castle by stealing a lantern bearing the enemy's family crest and making replicas to gain entry without a fight.
Japanese castles were designed to be difficult to navigate with winding routes leading to the inner compound and blind spots that provided constant surveillance. Nijō Castle in Kyoto was constructed with long nightingale floors which rested on metal hinges specifically designed to squeak loudly when walked over. Grounds covered with gravel provided early notice of unwanted intruders, and segregated buildings allowed fires to be better contained.
The world's first research centre devoted to the ninja was founded by Mie University in 2017. The center is located in Iga and offers a graduate master course that requires students to pass an admission test about Japanese history and be able to read historical ninja documents. On the 19th of June 2022, Kōka city announced the discovery of a written copy of Kanrinseiyo, the original source of the famous book on the art of ninja called Bansenshukai.