Every day, Michael MacCauley (Liam Neeson) follows a set routine before beginning his daily commute. He enjoys his time with his wife, Karen (Elizabeth McGovern), and their son, Danny (Dean-Charles Chapman), before hopping on the train to work, often chatting with familiar faces like Walt (Jonathan Banks).
Michael, who works in life insurance, faces a life-altering moment when his boss informs him that he's being laid off. After an unsuccessful attempt to convince his boss otherwise, he leaves the office feeling dejected. Later, he meets up with his friend Officer Alex Murphy (Patrick Wilson), a former partner from his days as a detective. Amidst their conversation, they catch a news segment detailing the mysterious death of a city planner, who supposedly leapt to his demise a few nights ago. Michael reveals to Murphy that he hasn't yet summoned the courage to share the news of his job loss with Karen. The encounter takes a turn when they learn that their colleague, Captain Hawthorne (Sam Neill), has taken over as captain, and he briefly joins their discussion.
On his train ride home, Michael becomes aware that a woman named Joanna (Vera Farmiga) appears to be watching him. After they exchange pleasantries, Joanna reveals to Michael the existence of a compartment on the train filled with $25,000 in cash, alongside an additional $75,000. She urges him to help find someone named "Prynne" at the last stop, Cold Spring. Before she leaves, Joanna drops a subtle hint suggesting she’s aware of his prior career as a cop.
Intrigued, Michael investigates the compartment, discovering the cash. However, when the train halts, a young woman attempts to claim the money, but Michael opts to keep it for himself. The woman hands him an envelope, warning him. Inside, he finds Karen's wedding ring, a chilling reminder of his family. With his phone lost, Michael borrows one from another commuter named Tony (Andy Nyman) to attempt calls to Karen and Murphy, but both efforts are fruitless. Suddenly, Joanna contacts Michael again, threatening that he must find Prynne or face dire consequences for his family's safety.
In desperation, Michael jots down a message for Walt to contact the police. However, just as he manages to do so, he receives a call from Murphy, who reveals that a witness using the alias "Prynne" claims to have seen the city planner's murder. After their conversation, Joanna’s voice surfaces once more, directing Michael’s attention outside. He witnesses a tragic incident where Walt is pushed into traffic, resulting in a fatal bus accident. Joanna warns him that this fate is what befalls those who try to evade her plans and instructs him to retrieve the bag that Prynne possesses and to plant a tracker on it.
Michael's heart races as he scans the other passengers for any signs of danger. He observes a girl named Gwen (Florence Pugh) with a suspicious bag but learns she’s merely carrying fake identification for her boyfriend. He soon spots a young man, Dylan (Killian Scott), who is on the phone and has a bag he follows. The confrontation escalates when Dylan attacks him for tailing him, though when Michael mentions Prynne, it piques Dylan's suspicion. They grapple until Michael, pretending defeat, slyly slips the tracker onto Dylan.
Shortly after, Joanna's call interrupts Michael again, instructing him to check beneath the floor in an empty train car. To his horror, he discovers Dylan’s lifeless body, a bullet wound in his head. Joanna accuses him of causing the boy's death by misidentifying him, intensifying Michael's panic as police begin to board the train after receiving reports of disturbances. Caught next to Dylan’s body as the officers investigate, Michael finds an escape route just in time, narrowly avoiding being trapped.
As the train approaches Cold Spring, Michael is filled with urgency. He identifies five unfamiliar commuters as potential Prynne suspects. Misguidedly, he follows a man playing cards with Tony, speculating that he is Prynne, only to find out he’s just a guitarist named Oliver (Kobna Holdbrook-Smith). The tense interaction becomes deadly when Oliver, seemingly working with Joanna, attempts to eliminate Michael. They fight violently, and Michael manages to turn the tables, ultimately stabbing Oliver before throwing him out of the train as it roars past another one.
With limited time left before reaching Cold Spring, paranoia grips Michael. He causes a malfunction in the train’s air conditioning, coaxing passengers into the cooler car to execute his plan. He suspects a nurse named Eva (Clara Lago), questioning her while holding her at gunpoint. Realizing she is innocent and merely trying to mend her relationship, he apologizes, sensing the weight of his actions.
As the train reaches Cold Spring, Michael’s adrenaline surges as he remembers a young woman named Sofia (Ella-Rae Smith) who briefly switched seats. Michael realizes that Prynne is connected to her, as the name references Hester Prynne from "The Scarlet Letter." She allegedly witnessed the murder and holds critical information that could expose the truth. Joanna, however, learns this and ominously declares that everyone’s lives are now at risk.
Trapped within an unfolding disaster, Michael alerts one of the conductors, Sam ([Colin McFarlane]), to stop the train. Despite their efforts on the emergency brake, the engineer’s demise hinders their progress. As the train derails, Michael leaps to safety, watching Sam perish in the wreckage but successfully unhooking one car from the others leaving him and the remaining passengers in a precarious situation.
Once order is restored, Michael approaches Sofia to discover she possesses a flash drive filled with incriminating information about the deceased city planner that she hasn’t dared to share with the police—highlighting just how deeply intertwined the police are with the crime. Meanwhile, outside, law enforcement believes Michael has taken the passengers hostage. Officer Murphy (Patrick Wilson) arrives, attempting to negotiate while suggesting that Michael may need to let people exit the train.
Realizing Murphy's true allegiance, Michael triggers a plan and cleverly distracts the police by switching trackers. When the truth surfaces regarding Murphy's accountability, their confrontation spirals out of control, leading to a tragic outcome.
After the dust settles, Michael is reunited with Karen and Danny, hearing that three conspirators have been apprehended. Sofia’s invaluable testimony aids in dismantling the crime syndicate. The passengers hail Michael as a hero, and Captain Hawthorne discusses his possible reinstatement as a detective.
In a riveting conclusion, Michael finds himself once again aboard the train. He spots Joanna (Vera Farmiga) lurking around and, while her facade remains, he confidently asserts that he knows her scheme. When she questions how this might conclude, Michael simply pulls out his detective badge, sealing a promise of justice and resolution.
