Following the mysterious disappearance of her father, Richard Croft, Lara Croft, portrayed by Alicia Vikander, has been making ends meet as a bike courier in London. With the guidance of Terry (Duncan Airlie James), who operates her martial arts club, she navigates her chaotic life. Richard, an esteemed expert on the ancient figure Himiko, recorded tapes detailing his ambitious research. Himiko, revered as Japan's first queen, wielded formidable dark magic that spread devastation across her empire. Her powerful generals ultimately captured and entombed her on a mystical island in the treacherous Devil's Sea, where she remains.
During a daring fox hunt, where she must outsmart a group of "hounds," Lara seeks a prize of 600 Pounds. However, her life takes a turn when she runs into trouble during a bike accident that involves a police car. Fortunately, Richard's business partner, Ana Miller, posts her bail, cautioning her that if she doesn’t claim her inheritance, her father's estate will be liquidated. Having been missing for seven years in Japan—with the Tokyo police having stopped their search five years prior—Lara is resolute in her belief that Richard is still alive.
Reluctantly, she visits her father’s company to sign the necessary papers, gaining entry into his office using a key hidden within a puzzle box. Here, she discovers a recorded message from Richard, delving into his research about the enigmatic Himiko, the queen of Yamatai, who was said to possess the power to control life and death, culminating in rivers flowing with blood. In his message, he advises Lara to destroy his research, but driven by curiosity, she opts to investigate further.
Struggling financially and without her inheritance, Lara pawns a precious jade pendant gifted by her father, receiving a meager 8000 pounds. Journeying to Hong Kong, she enlists Lu Ren as captain of the Endurance to navigate the treacherous waters to Yamatai, discovering through Richard's coded coordinates that Lu’s own father went missing alongside him.
As they near the island, Lara meticulously studies Richard's research, detailing the tomb's traps and challenges laid out by Himiko herself, including the treacherous Chasm of Souls and the formidable Faces of Himiko. However, during a tumultuous storm, their ship capsizes, leading Lara to wash ashore, where she is rescued by Mathias Vogel, leader of an expedition funded by the mysterious organization Trinity. This organization seeks to harness Himiko's supernatural power as a weapon, and Vogel claims to have slain Richard while intent on using his research to further his mission.
With a desperate escape aided by Lu Ren, who has also survived, Lara finds herself plunged into danger after a watery tumble. Regaining consciousness, she is propelled into a fight for survival, knocking out a Trinity guard who nearly discovers her. Wandering the island, she encounters a shadowy figure—her father, Richard, who reveals he has also been a captive on Yamatai.
Convincing him of her reality, Lara tends to her wounds, but the tension builds as Richard expresses his fury for her defiance against his wishes to obliterate his research. As Vogel, having deciphered Richard's diary, locates the entrance to Himiko's tomb but is unable to unlock it, Lara resorts to rallying forces with Lu and the local fishermen to create diversions and infiltrate the Trinity camp to reclaim her father's research.
Amid chaos, Richard strives to enter the tomb, but before he can act, Vogel persuades Lara to unlock it, fulfilling a lifelong ambition. As they enter the tomb, the realization dawns that the ancient site is a trap designed to ensnare its explorers, and within, they encounter Himiko's sarcophagus. However, chaos erupts when two soldiers come into contact with Himiko's remains, leading to their rapid disintegration due to a virulent affliction.
Ultimately, Lara realizes that Himiko willingly entombed herself to shield her people from harm, a sacrifice lost to time. In a desperate bid, Vogel shoots one of his infected men, desperate to claim the queen’s remains, but instead he is forced to settle for a sample. As the conflict escalates, Lara and Richard manage to overpower the remaining soldiers, but not before Vogel escapes, leaving Richard infected. With no cure available, he urges Lara to destroy the tomb to halt the spread of the deadly virus, setting off a bomb that seals the tomb—and dooms himself in the process.
A fierce confrontation ensues between Lara and Vogel, resulting in him meeting his end after she makes him swallow a piece of Himiko's remains, all while she is rescued by Lu and the fishermen, who commandeer a Trinity helicopter for their escape.
Returning to London, Lara officially claims her inheritance but uncovers shocking truths about Trinity’s involvement, discovering that their front organization is actually controlled by Croft Holdings. Suspecting that Ana Miller is complicit in Trinity's schemes, she realizes she has been manipulated into signing over control of her father’s business. With these revelations igniting her resolve, Lara prepares for her next adventure, determined to thwart Trinity's sinister plans.
