Snake Eyes saves the life of a man named Tommy, also known as Storm Shadow and is the future leader of the Arashikage clan, while he is hunting down the man who murdered his father. However, it is all a setup as Snake has agreed to steal a sacred jewel from Arashikage for Cobra, in exchange for information about his father`s killer. When Snake learns of Cobra`s true agenda, his loyatlies are put to the test and he starts questioning his revenge mission.