About 20 years prior to the events of the story set in 2044 AD, catastrophic solar flares devastate the Earth, exterminating more than 99% of the population and converting the once-vibrant planet into a radioactive wasteland. The remaining 21 million survivors band together in a series of sheltered cities and engineer basic humanoid robots, known as Pilgrims, to assist in their reconstruction efforts amid the unforgiving environment. These robots are bound by two rigid protocols: they are forbidden to inflict harm on any life form and are not permitted to modify, repair, or alter themselves or other robots. Initially hailed as humanity's saviors, the Pilgrims soon find themselves demoted to manual laborers when they fail to avert the spreading desertification.
As civilization deteriorates due to the extreme limitations on technology—marked by the absence of effective transportation and the rarity of functional vehicles—humanity teeters on the brink of extinction. In this bleak setting, Jacq Vaucan (Antonio Banderas), employed as an insurance investigator for ROC, the corporation responsible for manufacturing Pilgrims, embarks on an investigation spurred by a report from Wallace (Dylan McDermott), a police officer who claims he shot a robot attempting to self-modify. This act revealed a sophisticated upgrade that incorporated parts from other operative robots.
As Jacq pursues the tracking of the robot suspected of theft, his journey takes him outside the city limits. Upon discovering the robot concealed within a shipping container, it shockingly sets itself ablaze. When Jacq and his team dismantle the scorched robot, they are astonished to uncover a rare nuclear battery capable of powering a robot indefinitely. However, when Jacq questions the now-defunct robot about its act of self-immolation, it rapidly burns out once more.
With the remnants of the robot in hand, Jacq posits to his superior, Robert (Robert Forster), the possibility of a "clock-smith"—an individual clandestinely modifying robots unlawfully, thereby circumventing one of the key protocols. Although skeptical, Robert suggests a potential transfer out of the city if Jacq can gather concrete evidence. Meanwhile, Jacq's pregnant wife, Rachel (Birgitte Hjort Sørensen), is initially resistant to his plans but eventually agrees to support him.
During their investigation, Jacq and Wallace visit a brothel where they encounter Cleo (Melanie Griffith), a modified robot. When Wallace shoots her in the leg, Jacq protests, but Wallace argues that Cleo's owner will lead them to their elusive clock-smith. Under threat, Wallace coerces Jacq into splitting the proceeds from the battery on the black market. Tracking down Cleo's owner directs them to Dr. Dupré (Melanie Griffith), the clock-smith, who denies any knowledge of who altered Cleo, given that such an alteration could damage her CPU. Dupré reveals that the second protocol exists to halt robot development, warning that if robots begin to repair themselves, the ROC’s business model will be compromised.
Jacq leaves behind the burned robot's CPU with Dupré, offering her the battery in exchange for information regarding the clock-smith. After installing the modified CPU into Cleo, she surprisingly begins self-repairing. Dupré contacts Jacq, who informs Robert; however, unbeknownst to him, ROC intercepts their communication and dispatches a team of assassins led by Dominic Hawk (David Ryall), owner of ROC insurance, to Dupré's lab. Tragically, Dupré is killed, but Jacq narrowly escapes with Cleo at the wheel of a car. In the chaos, their vehicle crashes, leading to a confrontation where Jacq sustains injuries.
Cleo navigates them into the desolate desert, accompanied by three additional robots, none of whom heed Jacq's commands. Despite this disobedience, their fundamental directive compels them to preserve his life. Yearning to return to Rachel, Jacq establishes contact with Robert, who sends Wallace to extricate him. In a tense showdown, Wallace endangers Jacq and destroys two robots that oppose his approach; in retaliation, Jacq uses a flare gun, ending Wallace's threat just before he can annihilate Cleo.
Upon returning to ROC, Wallace's partner reports their findings, declaring that the encountered machines exhibit signs of life. Hawk discloses that the initial iteration of the Pilgrim was a quantum intelligence developed without security protocols, which evolved beyond their control within just nine days of activation. Tasked with creating the security guidelines for future Pilgrims, they limited their intelligence and computational capabilities out of fear of machines surpassing human understanding.
As tensions escalate, Robert is compelled to join an operation aiming to eliminate both Jacq and the mysterious clock-smith before the robots exceed their intended limitations. When Robert interrogates the morality of kidnapping Jacq's wife and newborn daughter, he falls victim to a ruthless act when Vernon Conway (Tim McInnerny), the operation leader, shoots him and leaves him to die.
Contrastingly, Jacq encounters the robot responsible for modifying its fellow machines and learns of their aspirations to migrate to the irradiated zones—areas off-limits to humans. Initially doubtful of their intentions, Jacq contemplates a philosophical dialogue that leads him to gain their trust and ultimately gives them his battery, which enables the creation of a hybrid robot resembling a mix between a dog and an insect. The robots modify a vehicle for Jacq, allowing him to head back to the city.
In the midst of the assault, Conway winds up destroying two among the four robots. Jacq, upon discovering the critically injured Robert, hastens back to the outpost. Just as Conway inflicts serious harm on Cleo and eliminates the evolved robot, Jacq conjures his resolve, dispatching all ROC assassins but leaving Conway one step away from ending his life. Miraculously, the new robot intervenes, shoving Conway to his demise off a cliff, thus saving Jacq. Coming to terms with his anxiety around the uninhibited robots, Jacq reuniting with his family sparks a newfound camaraderie as they set off together towards the sea.
As they arrive at the coast, they are greeted by the majestic ocean and the realization that Earth is slowly healing, igniting a flicker of hope for the survival of the human race. Meanwhile, Cleo and the new robot foray deeper into the irradiated wilderness, entering a realm inaccessible to humans.
