- "These converts are our foothold in this country."
- ―Alessandro Valignano.[src]
During the first half of the 16th century, the Templars had suffered numerous defeats at the hands of the Assassin Brotherhood. Around 1549, the Spanish Templar Francis Xavier set his sights on Japan, seeing an opportunity to spread both Christianity and Templar influence on the island.
However, the Templars' attempts to find new recruits were frequently hindered by the constant wars between clans, as well as their hostility toward outsiders. The Templars were also heavily opposed by the Japanese Assassins, who worked to prevent the spread of their influence in Japan and recruited individuals from the ranks of the ninja and samurai, such as Hattori Hanzō and Yamauchi Taka. The Assassins supported Tokugawa Ieyasu, one of the many warlords of the period, who similarly opposed the Templars' influence and, as such, tasked his former squire Chaya Shirōjirō Kiyonobu with reporting any Templar activity in the land.
Despite the opposition they faced, the Templars eventually managed to recruit, among others, Uesugi Kenshin, head of the Uesugi clan. Kenshin fought various battles with his rival Takeda Shingen, the owner of a Sword of Eden. Their rivalry ended when Shingen was assassinated in 1573 by the Tokugawa and the Assassins, and Kenshin himself was killed by the Assassin Hattori Hanzō in 1578.
Meanwhile, Alessandro Valignano, an Italian Jesuit missionary and a member of the Roman Rite of the Templar Order, was sent to aid fellow missionary Francisco Cabral, who was already doing missionary work in Japan. However, the two men despised one another almost instantly. Valignano used his Jesuit connections to scour Japan for Templar recruits, and upon Francisco Cabral confronting Valignano regarding this, Alessandro used his influence to force Cabral to resign from his post as Superior of the Jesuit Mission.
By the 1590s, the Templars had managed to recruit the kunoichi Mochizuki Chiyome, a noblewoman who had created an all-female group of ninja agents in her service as the spymaster of her uncle-in-law, Takeda Shingen. Through Chiyome, the Templars gained a vast information network that helped spread their philosophy throughout Japan. However, Chiyome was eventually assassinated by Hanzō after he tracked her down to her residence in Shinano, shortly before his own death in 1596 at the hand of Fūma Kotarō.
In December 2013, the Abstergo facility in Osaka was infiltrated by the Assassins, who, by then, had taken over a yakuza faction known as the Onmoraki-Gumi. The Assassins managed to steal a new type of Animus headset, which they later gave to the Assassin team led by Gavin Banks.