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's research on the lost city of Kitezh and the promise of immortality. Her father's partner, Ana, warns Lara that her father, Lord Croft's obsession with Kitezh, 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, who is 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 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 while climbing a mountain. Via radio contact, Lara urges Jonah to leave and not look for her.

After gathering resources to craft shelter and a bow, Lara discovers that Trinity has made a Soviet-era installation a base of operations in their search for Kitezh. Lara is caught trying to retrieve the book and is imprisoned with Ana. Konstantin forces her to reveal what she knows by slowly strangling Ana in front of her, but Lara cannot provide useful information. Upon realizing Lara does not know the whereabouts of the source, Ana reveals that she works for Trinity 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, and Trinity pursues them. During the chase, Lara is incapacitated and nearly drowns, but Jacob saves her, and she later agrees to aid him, and his people repel Trinity. Upon reaching the valley of the Remnant, Lara discovers that Jacob is their leader 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 seeks the Divine Source to cure herself. Jacob warns Lara that the Divine Source is real but not what she expects it to be. Lara's goal remains the same despite Jacob's warning, and she sets out to find the Atlas: an artifact that shows the way to Kitezh. Sofia, Jacob's daughter, warns Lara of the Deathless Ones, who guard the Atlas and kill trespassers. Lara finds the Atlas located in the archives beneath the ruins of a Cathedral building.

She recovers the artifact and is attacked by The Deathless Ones. She narrowly escapes and is later reunited with Jonah who was found by the Remnant and brought to the valley. He admits he spied on Trinity, but Konstantin was aware of his presence and followed him in the hope of finding Lara. After Lara discovers the path to Kitezh, Trinity forces return to the valley and attack. They take the Atlas and capture Jonah, shooting Jacob in the process. Lara returns to the Gulag to find Jonah.

She eventually does, but Konstantin mortally wounds him. Lara, along with some captured remnants from the Gulag bring 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, which looms over Kitezh, Lara is forced to enter the city on a dangerous path and encounters the Deathless Ones, the city's immortal guardians that keep the power of the source.

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 of Souls, the place that houses the Divine Source. With aid from Sofia and the Remnant, Lara battles her way through Trinity towards the Chamber of Souls, destroying Konstantin's helicopter. Konstantin survives the crash and 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 of Souls but is too late to prevent Ana from retrieving the Divine Source. Lara tries to reason with Ana to no avail.