Empire of Assassins is a story of family revenge and the bond of blood brothers. Tien Boa has trained for 15 years to avenge the death of the Zhang Heng family. The family responsible for this crime has just massacred the 10 rival martial arts groups and is now set to become unstoppable. After an unsuccessful assassination attempt targeted at the master of the family, Tien Boa must fight through a succession of family members to make his way to safety. He runs into Yu Fing, his betrothed and daughter of the master, and cannot bring himself to kill her. Fighting past her cousin and brother, he falls into a trap in the courtyard. Yu Fing stops her brother Ren Yi from killing him until they can find out who he is and why he came there.
Suspicious and believing him to be her dead childhood friend, Tien Boa, she secretly helps him heal. We learn that Ren Yi is Tien Boa's brother Tien Yong and that after his village was slaughtered, the master took Tien Yong as his son. The master now calls on Tien Yong to prove his loyalty to him and take revenge against this assassin, not knowing he is his brother.
During the battles to escape the castle grounds, Tien Boa learns that Ren Yi is his brother and refuses to kill him. Badly injured, he narrowly escapes with his life. Tien Boa goes into hiding in a village to heal. Yu Fing stops at nothing to find him and tells her brother Ren Yi that this man is their beloved Tien Boa.
Her father learns of her meddling and sentences Yu Fing to confinement in her room for one month. Tien Yong helps her to escape and she runs away to Tien Boa. She offers him a life apart from this revenge he is seeking, but their battle cannot end until the brothers are reunited to fight for the same side.