The game opens with a narration by William describing Amrita, a mystical golden stone found in abundance in Japan that is sought by the government of Queen Elizabeth I to secure victory over Spain. William was one of many pirates who were contracted by the queen to obtain Amrita, but afterwards was imprisoned to keep the Amrita a secret. While being held in the Tower of London, William breaks out with the help of his Spirit Guardian Saoirse, a being born from the prayers of his home village who saved him from death when he was a boy and now prevents him from dying. William is confronted by Edward Kelley, who is seeking Japan’s Amrita. Kelley attempts to kill William through the Tower’s executioner whom he corrupts with Amrita, where he then captures Saoirse with his own Ouroboros spirit, Kelley takes her with him to find Japan with William going in pursuit.