A young boy named Max Archibald experiences a tragic loss when his father, portrayed by Steven Allerick, is brutally murdered. Fast forward two decades later, this boy transforms into an incredibly skilled and deadly martial artist, now known as Snake Eyes and played by Henry Golding. His name originates from a harrowing incident where, during his father’s murder, he was forced to roll a pair of weighted dice that sealed his father’s fate – rolling double ones resulted in death.
In the underground fighting scene of Los Angeles, the wealthy Yakuza boss, Kenta Takamura, played by Takehiro Hira, encounters Snake Eyes. Kenta proposes a deal: he will help Snake Eyes uncover his father's killer if he agrees to work for him. Eager for vengeance, Snake Eyes readily accepts. However, when Kenta demands he kill a man who betrayed him, Snake Eyes courageously refuses — this man, Tommy, played by Andrew Koji, has shown him kindness, unlike most of Kenta's men. Instead, he aids Tommy in his escape, causing friction between the two factions.
Tommy, motivated by revenge against Kenta, is also in a dangerous game; their rivalry traces back to Kenta's attempt to eliminate Tommy in their bid for leadership of the revered Arashikage clan, a society of ninjas committed to justice and order. Having failed at killing him, Kenta has resorted to smuggling weapons to overthrow the clan, with Tommy secretly working to thwart these nefarious plans.
In a gesture of gratitude, Tommy brings Snake Eyes to his dojo in Tokyo, hoping to induct him into the Arashikage clan. The clan's leader, Sen, played by Eri Ishida, allows Snake Eyes to undergo three trials to prove his worthiness. Among the mentors overseeing the trials are Hard Master (portrayed by Iko Uwais), a formidable uncle to Tommy, and Blind Master (played by Peter Mensah), who is revered within the clan.
Initially met with skepticism by Akiko (played by Haruka Abe), who is responsible for clan security, Snake Eyes ultimately earns her trust by revealing the traumatic details surrounding his father's death—a truth that had remained concealed. Yet, unbeknownst to all, Snake Eyes harbors a secret plan that threatens the very foundation of his newfound clan. His inner turmoil intensifies when it's revealed that Kenta orchestrated Tommy's betrayal to manipulate Snake Eyes into stealing from the clan’s most cherished possession, the "Jewel of the Sun."
The jewel, a treasured artifact said to possess magical abilities, was gifted by the Sun God, and the clan has vowed to protect it without ever utilizing its power for harm. As Snake Eyes grapples with his conflicting loyalties, he excels at the initial trials despite the weight of his guilt concerning Tommy's destiny as well as his own thirst for revenge. The first trial, aimed at testing his combat skills, sees him ultimately succeed by diplomatically exchanging bowls of water with his mentor, Hard Master, while the second trial confronts him with the painful memories of his father's murder.
As tensions escalate with the resurgence of Kenta aligning with the terrorist group Cobra, Snake Eyes meets with his nemesis again, only to reject Kenta's use of him as a pawn to fulfill Cobra's plans, despite being coerced—Kenta holds Snake Eyes' father's killer captive and will only release him if Snake Eyes acquires the jewel.
The final trial, testing the purity of his heart against sacred anacondas, is fraught with peril. Snake Eyes falls victim to their attack due to his hidden motives, but Akiko intervenes just in time. In a moment of confrontation, Snake Eyes comes clean to the clan but cleverly conceals the full extent of his deception, resulting in his expulsion.
Despite this, he returns stealthily, leveraging his knowledge of the temple’s layout to swipe the jewel and deliver it to Kenta. The Yakuza boss, intoxicated by the jewel's magic, vows it will be delivered to Cobra upon decimating the Arashikage clan. However, as Snake Eyes encounters his father's killer, he finds clarity and, in a surprising act of mercy, spares the man, grappling with the cost of his vengeance.
Ultimately, Snake Eyes allies with Tommy and the clan, including Scarlett (played by Samara Weaving), a member of G.I. Joe, to fend off Kenta's forces. Despite their combined efforts, Kenta's betrayal culminates in chaos, and with the jewel in his possession, he aims to eliminate the clan forever. However, in an intense confrontation, Snake Eyes traps Kenta in a pit of anacondas, where justice is served as Kenta is devoured, his malevolence recognized by the sacred creatures.
In the aftermath, Sen strips Tommy of his leadership role within the clan for using the jewel, leading him to renounce his family ties and vow vengeance on Snake Eyes. The film closes with a glimmer of new beginnings as Snake Eyes and Scarlett discuss his father’s legacy and the opportunity to join G.I. Joe.
The post-credits tease a dramatic shift with the Baroness recruiting Tommy into Cobra, revealing his new identity as Storm Shadow.
