One year after the events of Tomb Raider, Lara Croft is struggling to explain her experience of the supernatural on Yamatai. Looking for answers, she turns to her late father's research into the lost city of Kitezh and the promise of immortality. Her father's partner Ana attempts to warn her off as his obsession with Kitezh drove him to ruin and suicide. Lara ignores her and organizes an expedition to Syria, hoping to uncover the tomb of the Prophet of Constantinople (modern day Istanbul), a key figure in the legend of Kitezh. Although successful, the tomb is empty, and Lara is interrupted by Trinity—an ancient order of knights that now exists as a paramilitary organization investigating the supernatural—and their leader Konstantin. As she flees, Lara discovers a symbol etched into the tomb that she links to a book on Russian religious history in her father's study. A Trinity assassin steals the book, prompting Lara and her friend Jonah to give chase in Siberia. When the two are separated after an avalanche, Lara is forced to go on alone.
Lara discovers that Trinity has taken over a Soviet-era mining installation as a base of operations in the search for Kitezh. She is caught attempting to retrieve the book and placed in a prison cell with Ana, who is revealed to be Konstantin's sister and a spy for Trinity. The two interrogate her as to the whereabouts of the "Divine Source", an artifact believed to grant immortality. Lara escapes, and in the process aids Jacob, a mysterious stranger who leads her through the mines into the valley beyond.
Jacob is revealed to be the leader of the Remnant, the descendants of the followers of the Prophet of Constantinople. As Lara aids in their resistance against Trinity, she begins to learn more about the Prophet and the lost city of Kitezh. After being branded a heretic and pursued by the Order of Trinity, the Prophet and his followers resettled in Russia, where they built Kitezh. However, spurred on by agents of Trinity, the Mongol Hordes led by Genghis Khan attacked the city, and the Prophet was forced to sacrifice it to protect the Divine Source. The Remnant escaped and settled in the area, vowing to defend the city's secret. Jacob warns her that although the Divine Source exists, it is not what she expects it to be. Konstantin's forces repeatedly attack the Remnant, believing them to be heretics and justifying the slaughter as God's will. However, Lara discovers that Ana is dying and has been manipulating her brother to find the Divine Source and save her.
Jacob and Lara decide that the only way to protect the Divine Source is to retrieve it before Trinity can. In order to do this, Lara recovers the Atlas, an artifact that serves as a map of Kitezh. She is reunited with Jonah, who has been spying on Trinity forces and they locate the path into the city. However, Konstantin has been aware of Jonah's presence and let him go free in the hopes that he would lead Trinity to Lara. Jonah is kidnapped with the Atlas, compelling Lara to rescue him. The attempt ends in disaster when Konstantin stabs him, knowing that Lara will prioritize his rescue and giving Trinity a head start. Lara takes Jonah to Jacob, who reveals himself to be the Prophet when he miraculously heals Jonah.
With Trinity advancing on the glacier that rests over Kitezh, Lara is forced to enter the city through the Path of the Deathless where she encounters the Deathless Ones, the immortal guardians of the city. Following the journals of a Trinity agent embedded in the Mongolian forces, Lara realizes the truth of Jacob's warning: the Divine Source grants immortality, but at the cost of their sense of self. The Deathless Ones are the immortal inhabitants of Kitezh, forced to defend the city for eternity. As Lara enters Kitezh, the Remnant rally to attack the Deathless Ones, giving her time to reach the heart of the city. She is attacked by Konstantin and mortally wounds him; he dies in disbelief that he was not carrying out God's will, but Ana's. Before his death, he claims that Lara's father did not commit suicide, but was in fact murdered by Trinity. Lara is too late to stop Ana from retrieving the Divine Source, but wrests it from her before Ana can use it. Lara destroys the Divine Source, killing the Deathless Ones, but Jacob loses his immortality. However, he is happy that his time has finally come and thanks Lara for bringing his end as he peacefully disintegrates.
In the aftermath, Jacob's daughter Sofia takes over the Remnant. Jonah recovers from his wounds and joins Lara in planning their next expedition, with Lara vowing to investigate more of the world's mysteries as well as thwart Trinity's plans. A post-credits scene shows Lara and Ana leaving Russia, two weeks before Lara returned to the manor. Lara asks Ana if her father was murdered by Trinity, which she confirms, but she is shot and killed by a sniper working for Trinity before she can reveal anything else. The sniper asks his unseen superior about killing Lara, but is told to stand down for the time being.
Baba Yaga: The Temple of the Witch The Baba Yaga downloadable content sees Lara investigating a disturbance within the Soviet mining facility. After fighting off a Trinity patrol, she discovers a young girl named Nadia hiding in a sawmill. Nadia confides in Lara, recounting her search for her grandfather, Ivan. Ivan has disappeared while trying to enter the Wicked Vale, a valley rumoured to be haunted by Baba Yaga, a witch from Russian folklore. Ivan blames the witch for the death of his wife and seeks to kill her. Lara is skeptical of Baba Yaga's existence, but as Nadia is injured, she agrees to enter the Wicked Vale and locate Ivan.
Once in the Vale, Lara is exposed to a rare pollen with potent hallucinogenic properties. After stumbling through a forest, tormented by visions of her father's suicide, she encounters Baba Yaga and a pack of demonic wolves. Lara narrowly escapes with her life and finds herself in a small Soviet-era outpost. There she unearths evidence of a secret Soviet biological weapons project that attempted to harness the pollen as a weapon; however, the project came to an abrupt end after the researchers—including Serafima, a biochemist imprisoned in a nearby gulag—succumbed to the hallucinations.
Realizing that Serafima resented her captors, Lara correctly deduces that she had successfully weaponized the pollen and developed an antidote and kept her research secret from the military. With Nadia's help, Lara synthesizes a rudimentary antidote from Serafima's recipe and returns to the Wicked Vale. Resisting the effects of the pollen, Lara finds Ivan injured at the entrance to Baba Yaga's lair. Unable to leave the Wicked Vale so long as Baba Yaga continues to control it, Lara ventures on to confront the witch and is forced to battle Baba Yaga under the effects of the pollen. Lara prevails, destroying the source of the weaponized pollen. Baba Yaga is revealed to be Serafima, who was led to believe that her husband, Ivan, was dead, and so used the pollen to become Baba Yaga and torment her captors in revenge. With Ivan, Serafima and Nadia reunited, Lara leaves the Wicked Vale.
Cold Darkness Awakened The Cold Darkness Awakened content sees Lara enter a decommissioned Soviet weapons bunker that has been breached by a Trinity patrol. Trinity have inadvertently released an unstable pathogen into the air, which causes the people it infects to regress to a zombie-like state. Men are particularly vulnerable as the virus stimulates testosterone and adrenaline production. The pathogen was created by a Soviet researcher with the intention of creating an army of unstoppable super-soldiers, but all of his experiments ended in failure. Following an accident that released the pathogen, he died in the facility, proud that he had at least created a weapon to protect his homeland. With Sofia and Nadia providing support from a helicopter, Lara attempts to find the source of the pathogen before an enormous cloud is released into the atmosphere and contaminates the Remnant valley.
The three women hatch a plan to channel the pathogen from three towers into the central tower, and cause it to explode, which will hopefully burn off the toxin. Lara shuts down each tower while collecting equipment, rescuing female prisoners and eliminating waves of the infected Trinity soldiers, and finally enters the core tower. While fighting off the infected soldiers, she triggers a catastrophic explosion and jumps from the tower to Nadia and Sofia's helicopter. Nadia and Lara watch the explosion as they fly to safety. Although the resulting fire burns the remaining reserves of the pathogen, documents found throughout the facility reveal that the release was no accident; Trinity reactivated the facility to acquire a sample of the pathogen, and an agent of Trinity escaped with it before the bunker was destroyed.