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Snake Eyes, a tenacious loner, is welcomed into an ancient Japanese clan called the Arashikage, who teach him the ways of the ninja and provide him home. But when secrets from his past are revealed, his honor and allegiance will be tested.

After saving the life of their heir apparent, tenacious loner Snake Eyes is welcomed into an ancient Japanese clan called the Arashikage where he is taught the ways of the ninja warrior. But, when secrets from his past are revealed, Snake Eyes' honor and allegiance will be tested - even if that means losing the trust of those closest to him.

A young boy (Max Archibald) is orphaned when his father (Steven Allerick) is murdered. Twenty years later, the boy has grown into a talented and deadly martial arts fighter, driven by a desire to avenge his father. To conceal his true identity, he calls himself "Snake Eyes" (Henry Golding), a name inspired when his father's murderer forced him to roll a pair of weighted dice to determine his fate, killing him when he rolled double ones.

Wealthy Yakuza boss Kenta Takamura (Takehiro Hira) discovers Snake Eyes in an underground fighting circuit located in Los Angeles. Kenta offers to find his father's killer if Snake Eyes will work for him, to which Snake Eyes accepts. When Snake Eyes is asked to prove his loyalty by shooting a man who betrayed Kenta's trust (Kenta accuses him of being an undercover spy), Snake Eyes refuses (Tommy had been kind and fair to Snake Eyes in Kenta's organization, unlike the rest of his troops) and instead helps the traitor escape. Tommy wants to kill Kenta and refuses to escape without killing him. Snake Eyes has to intervene multiple times to keep Tommy safe and eventually Kenta has to back off when the police arrive. Snake Eyes is stabbed in the attacks.

The traitor is Kenta's cousin, Tomisaburo "Tommy" Arashikage (Andrew Koji). Tommy and Kenta were both in line to lead the Arashikage clan, an ancient ninja society devoted to preserving order and fighting evil. Kenta sought to kill his cousin, but failed and was banished. Kenta was therefore smuggling guns into Japan, via US, to stage a coup against the clan and Tommy was undercover to stop him.

Grateful to Snake Eyes, Tommy takes him to his ninja Dojo in Tokyo, Japan and asks that he be initiated as a member. The current Clan Arashikage leader, Sen (Eri Ishida), Tommy's grandmother, agrees to let Snake Eyes undergo three trials to determine if he is worthy. Hard Master (Iko Uwais), A formidable mentor of the Arashikage clan and the uncle of Tommy. Blind Master (Peter Mensah), A blind mentor of the Arashikage clan.

The clan's head of security, Akiko (Haruka Abe), does not trust Snake Eyes at first, but he wins her trust by revealing his father's murder and explains that is why there is no recorded history of him. Unbeknownst to anyone, Snake Eyes plans to betray his new allies. Tommy's attempted murder and escape is shown to have been staged by Kenta in order to get Snake Eyes close enough to steal the clan's most sacred treasure, the "Jewel of the Sun", which has magical powers. Tommy tells Snake Eyes that the jewel was a gift from the Sun God and the clan is sworn never to use it, even to kill evil, and to only protect it.

Snake Eyes finds himself increasingly torn between his guilt over betraying Tommy, the clan, and his overwhelming desire for revenge. He passes the first two trials with his exceptional talents. First trial is to snatch a bowl of water from Hard master's hands in combat, without spilling your own bowl of water, in 4 attempts. Snake Eyes fights and loses 3 times and then finally succeeds by simply asking Hard Master to exchange their bowls of water.

The 2nd test is an illusion that brings Snake Eyes face to face with his father's killers on that night when they burnt his house down. Snake Eyes is furious and attacks but is gunned down. He is approached by his father, who tells him it was not his fault, as he was just a kid. Snake Eyes unburdens himself of the guilt of his father's death.

Snake Eyes and Tommy learn that Kenta is back in Tokyo and aligning with the terrorist revolutionary organization Cobra. Snake Eyes meets Kenta again, in secret, and says he has no intention to work for terrorists. Kenta explains to Snake Eyes that he is tasked to steal the jewel on behalf of Cobra. Cobra, through their liaison, the Ana DeCobray / Baroness (Ursula Corberó), has been arming Kenta with weapons so that he can seize control of the Arashikage clan. Kenta and Baroness inform Snake Eyes that they have his father's murderer imprisoned and will release him if Snake does not secure the jewel for them.

The third and final trial requires his spirit to be tested by sacred anacondas, who can sense if he is truly pure of heart. Due to Snake Eyes' secrets, the snakes attack him, but Akiko saves him from being killed. Confronted by the clan, Snake Eyes admits that he has not been entirely honest but manages to hide the true reason he is there and is expelled. Snake Eyes later returns in secret and steals the jewel using his knowledge of the clan's temple, delivering it to Kenta. Kenta tastes the magic of the jewel and promises to hand it over to Cobra once he has destroyed the Arashikage clan. Snake Eyes receives his reward for stealing the jewel: his father's killer, who turns out to be a Cobra agent. Having realized what his blood-lust has cost him, Snake Eyes spares the man and instead goes back to the Arashikage clan to warn them of Kenta's attack.

Tommy puts aside his anger and let's Snake Eyes assist him and the clan's warriors, including Major O'Hara / Scarlett (Samara Weaving), a member of the international peacekeeping organization G.I. Joe, in fighting off Kenta's men. Baroness helps Kenta corner Sen and the clan is effectively defeated. After Kenta admits that he has no intention of handing over the jewel, the Baroness forms a temporary alliance with the Arashikage clan and Scarlett. With his men defeated, Kenta loses the jewel to Tommy, who overwhelmed with fury tries to use its power to kill Kenta. Kenta manages to escape, but Snake Eyes traps him in the anaconda pit, where the snakes devour Kenta upon sensing his evil spirit. The snakes then judge Snake Eyes to now be pure of heart for forgoing his lust for revenge, thus now being worthy of joining the clan.

After the battle, Sen strips Tommy of his birthright to lead the clan for breaking his vow never to use the jewel. Blaming Snake Eyes for this, Tommy forsakes the clan and family, vowing to kill Snake Eyes should they ever meet again. Snake Eyes meets with Scarlett who, after explaining that his father was a G.I. Joe agent, offers him a chance to become a Joe.

In a mid-credits scene, on a private jet leaving Japan, the Baroness recruits Tommy into Cobra, and Tommy has renamed himself "Storm Shadow".