By 1257, knowledge of the country had reached the western world. Altaïr Ibn-La'Ahad suggested spreading rumors that his Apple of Eden had been transported to Japan or Cyprus to draw away the Templars from looking for it beneath Masyaf.
After several defeats by the Assassins in Europe during the early 16th century, the Templars led by Francis Xavier sought to spread their influence in Japan. Despite the difficulties posed by the the island's warring states, they recruited a few Japanese sympathizers like Mochizuki Chiyome. The Assassins responded by recruiting rival ninjas like Hattori Hanzō.
In 2013, the Assassin headquarters in Osaka was attacked by the yakuza faction known as Onmoraki-Gumi, resulting in the death of Mentor Kenichi Mochizuki. As retaliation, his wife Saeko Mochizuki led an attack on the yakuza faction, taking over the organization and using it as a front for the Assassin activities and leading as the Japanese Brotherhood's new Mentor.
- In his cryptic messages, Clay Kaczmarek made references to the Yonaguni Monument, and drew imagery of Mount Fuji, Nara-style pagodas, and a torii.