One year after the events of Tomb Raider, archaeologist Lara Croft is struggling to explain her experience of the supernatural on Yamatai and is experiencing posttraumatic stress disorder. Looking for answers, she turns to her late father Lord Croft’s research on the lost city of Kitezh and the promise of immortality. Ana, Lord Croft’s partner, warns Lara that her father’s obsession drove him to ruin and suicide. Lara ignores her and organizes an expedition to the Forgotten Cities in northwestern Syria, hoping to uncover the tomb of the Prophet of Constantinople, a key figure in the Kitezh legend. The tomb is empty, and Lara is interrupted by Trinity—an ancient order of knights turned paramilitary organization investigating the supernatural—and their task force leader, Konstantin. As she flees, Lara discovers a symbol etched into the tomb, which she links to a book on Russian religious history in her father’s study at Croft Manor. She learns of an artifact called the Divine Source, said to be capable of granting immortality. After arguing with her friend Jonah Maiava regarding the artifact’s existence, a Trinity assassin infiltrates the manor and steals the book, prompting the two to go to Siberia.
In Siberia, Lara and Jonah are separated by an avalanche. Continuing alone, Lara discovers that Trinity has made a Soviet-era installation a base of operations in their search for Kitezh. She is caught trying to retrieve the book and is imprisoned with Ana. Konstantin slowly strangles Ana in an attempt to force Lara into revealing what she knows. Upon realizing Lara does not know the whereabouts of the source, Ana reveals herself as a Trinity agent and that Konstantin is her brother. She asks Lara to join Trinity, but she refuses and is taken to the Gulag cells, where she meets a man named Jacob. Together they escape the Gulag with Trinity in pursuit. During the chase, Lara is incapacitated and nearly drowns, but Jacob saves her, and she later agrees to aid him and his people in repelling Trinity.
Upon reaching a valley of hot springs, Lara discovers that Jacob is the leader of its inhabitants, the Remnants, and that they are descendants of the Prophet’s followers. Trinity repeatedly attacks the Remnant, justifying the slaughter as God’s will. However, Lara discovers that Ana suffers a terminal illness and is seeking the Divine Source to cure herself. Jacob warns Lara that the Divine Source is real but not what she expects it to be. Lara remains undeterred and sets out to find the Atlas, an artifact that shows the way to Kitezh. Sofia, Jacob’s daughter, warns Lara of the Deathless Ones, the immortal guardians of Kitezh. Lara finds the Atlas located in the archives beneath the ruins of a Cathedral, and is later reunited with Jonah, who was found by the Remnant and brought to the valley. After Lara discovers the path to Kitezh, Trinity forces return to the valley, take the Atlas and capture Jonah. Lara returns to the Gulag to find Jonah, but Konstantin mortally wounds him. Lara brings Jonah to Jacob, who heals him. Upon witnessing Jonah’s rapid recovery, Lara realizes that Jacob is the Prophet, given immortality by the Divine Source.
With Trinity advancing on the glacier looming over Kitezh, Lara is forced to enter the city on a dangerous path. Reading journals written by a Trinity agent, Lara realizes the truth of Jacob’s warning: the Divine Source bestows immortality at the cost of one’s self. Trinity breaks through the ice and enters the chamber that houses the Divine Source. With aid from Sofia and the Remnant, Lara battles her way through Trinity towards the chamber. Konstantin ambushes Lara, but she mortally wounds him. Before he dies, Konstantin reveals that Lara’s father did not commit suicide but was assassinated by Trinity. Lara enters the chamber but Ana has already retrieved the Divine Source. Jacob and Lara try to reason with Ana to no avail. As the Deathless Ones close in, Ana activates the Divine Source but is overwhelmed by its power, giving Lara a chance to pick it up and smash it to pieces, causing the Deathless Ones to perish. Jacob’s immortality is lost but is happy his time has finally come. He assures Lara she has made a difference and peacefully disintegrates.
Two weeks later, at Croft Manor, Lara and Jonah overlook their next expedition. Lara vows to investigate more of the world’s mysteries and thwart Trinity’s plans. In a post-credits scene, two weeks before Lara and Jonah leave Siberia, Lara asks Ana if she killed her father. Ana denies it, admitting that Trinity gave her the order. Before she can reveal anything else, she is killed by a sniper, who asks his unseen superior about killing Lara and is ordered to stand down for the time being.