Set in the year 1987, the story begins with the high-stakes actions of US Navy Lieutenant Troy "Assassin" Kelly, played by Ryan Reynolds, who demonstrates his skill and bravery by rescuing his wingman who is unable to land on an aircraft carrier. Following this successful landing, Kelly is recruited for a highly sensitive and covert reconnaissance mission over Russian territory. He is tasked with flying the advanced SR-71 Blackbird alongside US Air Force pilot Major Sanders. However, the mission takes a tragic turn when they are intercepted by a MiG fighter jet, resulting in the death of Major Sanders. In a desperate and bold maneuver, Troy forces a collision with the MiG before ejecting from his aircraft.
Upon landing in hostile territory, Troy is discovered and rescued by Nikolai "Nick" Ustinov, portrayed by Kenneth Branagh. Nick is a former KGB officer who possesses a deep fascination with American culture. Haunted by his past service in the KGB, Nick harbors a strong desire to help Troy and dreams of one day living in the United States. Although Troy initially attempts to flee on his own, Nick saves him once more, shielding him from the relentless search efforts led by the KGB and the formidable Alexander Volkov.
A tentative alliance is formed when Troy agrees to help Nick secure asylum in the US in exchange for Nick's help in escaping Russia. Their journey is fraught with danger; while traveling by train, they are spotted by the Russian military, forcing them to leap from the moving vehicle to evade capture. They find temporary refuge in a dacha, from where they contact the US Embassy in Moscow to arrange a meeting. However, their communications are intercepted, and Volkov becomes aware of their plans.
Once they reach Moscow, Troy and Nick visit Nick's estranged daughter, Anna, played by Maria Bakalova. Their reunion is cut short when Volkov's agents launch a violent attack on her apartment, forcing the group to flee to a safe house owned by Anna. During this time, Anna reveals a personal secret to Troy: she is a lesbian, a fact that is illegal in Russia and the primary reason for her estrangement from her father. Nick admits that he was already aware of this, and it was one of the motivating factors behind his decision to leave the KGB. With Troy's encouragement, Nick and Anna finally reconcile. Before parting, Anna leaves her father a photograph of herself with her girlfriend and a poignant message asking him to call her once he arrives safely in America.
The following morning, a devastating blow occurs when Troy contacts the embassy, only to learn that they will not provide asylum for Nick. While Troy still intends to meet at the embassy, Nick overhears this news and feels deeply betrayed. In a moment of desperation, Nick hands Troy over to Volkov. During a brutal interrogation, Volkov attempts to coerce them into signing false confessions. To break Troy's spirit, Volkov presents a memo proving that the US Navy knowingly exposed shipyard workers to carcinogenic asbestos—a tragedy that directly affected Troy's father. Despite the emotional pressure, Troy refuses to sign.
In a sudden turn of events, Nick pretends to cooperate but uses a pen to stab Volkov, allowing him and Troy to break free. In their daring escape, the duo manages to steal a mobile nuclear launcher. As they flee, Troy reveals the true story behind his call sign, "Assassin," leading to a genuine reconciliation between the two men. They make their way to the airport and hijack a Type ATR 42 aircraft. As they take off, Volkov boards the plane in a final attempt to stop them, but Troy manages to kill him by throwing him from the aircraft.
Realizing they cannot reach friendly territory in Finland, Troy uses his leverage to negotiate full immunity for Nick, allowing them to land safely on the USS Carl Vinson. In the aftermath of these events, Troy takes a principled stand by testifying before Congress regarding the Naval memo and the asbestos cover-up, which results in him being placed on indefinite leave from the Navy. The story concludes on a hopeful note, with Troy and Nick sharing a meal at McDonalds and planning a road trip across the United States in Nick's RV.