During the reign of the Tang dynasty in China, a secret organization called "The House of the Flying Daggers" rises and opposes the government. Leo is a police officer who sends officer Jin to investigate a young dancer named Mei, claiming that she has ties to the "Flying Daggers" organization. Leo ends up arresting Mei, only to have Jin break her free in a plot to gain her trust and lead the police to the new leader of the secret organization. But...

Cynthia is a young Chinese woman in love with Itami, a Japanese man about to be sent home for military service. A devasted Cynthia moves back to Shanghai only to witness the death of her elder brother during an attack by the Japanese extreme right. She changes her name to Ding Hui and joins a secret resistance group code-named Purple Butterfly. This will be the same group that, years later, will plot to assassinate Itami.

Through a revolutionary technology that unlocks his genetic memories, Callum Lynch experiences the adventures of his ancestor, Aguilar, in 15th Century Spain. Callum discovers he is descended from a mysterious secret society, the Assassins, and amasses incredible knowledge and skills to take on the oppressive and powerful Templar organization in the present day.