Plot
Living on the run, a young boy and his father are found by their sinister pursuers. Forced to roll dice to determine his fate, the father is murdered after rolling double ones, but his son escapes.
Twenty years later, the boy has adopted the name "Snake Eyes" and is discovered by Yakuza boss Kenta Takamura, competing in an underground fighting circuit. With the promise of help finding his father's killer, he agrees to join Kenta's criminal organization, and is asked to execute a man who infiltrated the gang, but helps him escape instead.
The man is Kenta's cousin Tommy, who reveals that they were both in line to lead the Arashikage clan, an ancient ninja society. Banished after trying to have Tommy killed, Kenta still seeks control of the clan. Grateful to Snake Eyes, Tommy brings him to his family's dōjō in Tokyo to be initiated. Tommy's grandmother Sen, the clan's current leader, agrees to let Snake Eyes undergo three trials to prove his worth.
In his first test, Snake Eyes is unable to seize a bowl of water from the clan's Hard Master; realizing this is a test of humility, he succeeds by respectfully asking instead. Unbeknownst to the clan, Snake Eyes has been tasked by Kenta with betraying Tommy; their escape was staged to allow Snake Eyes to win Tommy's trust, and to steal the clan's sacred "Jewel of the Sun".
The clan's head of security, Akiko, distrusts Snake Eyes, but she accompanies he and Tommy on a raid of Kenta's gang. They learn through an ally, Major Scarlett O'Hara, that Kenta is allied with the terrorist organization Cobra. Snake Eyes confronts Kenta and his Cobra liaison, the Baroness, who warns that stealing the jewel is the only way they will lead him to his father's killer.
The clan's Blind Master administers Snake Eyes' second test, a vision of his father, and he bonds with Akiko after telling her about his father's death. For his final trial, he faces the clan's gigantic, sacred anacondas. Sensing he is not truly pure of heart, the snakes attack, but he is saved by Akiko. Snake Eyes conceals his deception, but admits to having vengeance in his heart, & his lifelong search for his father’s murderer. He is allowed to live, but is expelled from the clan. He bids farewell to Tommy as blood brothers, but breaks into the clan's temple that night, subduing Akiko and stealing the jewel.
He delivers it to Kenta, who agrees to give it to Cobra once he has used it to take over the Arashikage. Snake Eyes receives his reward — his father's killer, a former Cobra agent — and forces him to roll his own dice, but spares his life and returns to warn the Arashikage. Tommy puts aside his anger when Snake Eyes comes to his aid, as Kenta uses the jewel's fiery magical powers to lay waste to the dōjō. Scarlett arrives to fight off Kenta's men, but she and Sen are captured.
A power-hungry Kenta refuses to hand over the jewel, prompting the Baroness to agree to a temporary alliance with Scarlett and the clan. With his men defeated, Kenta loses the jewel to Tommy, who tries to use its power to kill him. Kenta escapes, but Snake Eyes traps them both in the anaconda pit, where Kenta is devoured. The snakes now judge Snake Eyes as pure of heart, worthy of joining the clan.
Sen strips Tommy of his birthright for breaking the family's vow never to use the jewel. Forsaking the clan and blaming Snake Eyes, Tommy vows to kill him should they ever meet again. As Snake Eyes sets out to find him, Akiko gives him a black outfit and helmet, and Scarlett informs Snake Eyes that his father was a member of international peacekeeping organization, G.I. Joe, and invites him to become a fellow Joe. The Baroness invites Tommy to join Cobra, and he declares a new name for himself: "Storm Shadow".
