Lara is climbing up a snowy mountain in Siberia, Russia with her friend Jonah Maiava and a small team. They have come to a point where the team won't follow them anymore and so the two continue on alone. They are searching for the lost city of Kitezh but the remainder of the journey is dangerous as a storm closes in. An avalanche separates the two, and despite running away from it as best as she could, Lara is knocked off her feet and buried in the snow.
A flashback to two weeks earlier shows Lara returning to her apartment in London. She sees a light from a flashlight inside; someone has broken in and is going through her research. Lara enters her home cautiously, closes the window and heads over to her research table. After a moment, she hears someone walking closer down the corridor, so she grabs a climbing axe, stands alert by the door and begins to swing it. She is relieved to see that it is Ana, her stepmother and tells her that she will continue her father's quest of uncovering the myth of the immortal soul. Ana tries to talk her out of it but Lara has made up her mind.
On the Northwest border of Syria, Lara has hired a driver to take her to her location but he was bought out by someone else. A helicopter hones in on them and opens fire, killing the driver. The vehicle rolls off the road but Lara scrambles out of it before it explodes. Lara is soon able to get to her feet and then begins her search for the lost tomb of the Prophet. She finds his tomb but his sarcophagus is empty. Noise from above tells Lara that she is not alone and she hides inside the sarcophagus. Men begin to rappel down ropes and the leader tells the soldiers that charges have been placed. When soldiers open the lid, she jumps up with her pistol aimed at him. He walks towards her and questions her for the artefact's whereabouts. Feeling threatened, Lara sneakily takes the charges device and uses it. The ceiling collapses and water begins to fill the corridors, so Lara makes her retreat.
Returning to Croft Manor, Lara is sat on the floor in her father's study, gathering research from papers and books. She hears a door opening and footsteps, and is happy to see Jonah. He asks if she had found the Prophet's Tomb, and she informs him that she had but was followed by a group called 'Trinity'. She reads to him a passage which says that Kitezh disappeared beneath a lake in the 12th century on the eve of a Mongol invasion and that Kitezh was linked to the Prophet and the Divine Source. He tries to talk her out of going to Siberia, to no avail, so he leaves but moments later, an intruder enters the room and Lara fights him. Jonah returns but the man jumps out of the window with a book of research. Lara convinces Jonah to join her in Siberia to find the Divine Source.
Back in Siberia, present day, Lara emerges from under the snow and answers Jonah's call on the radio, telling him to not come after her. She finds an abandoned camp and makes a fire. Noise on the radio tells Lara that she is no longer on her own in her search for the Source, and she repairs an old bow that had been left behind. Soon enough she continues searching for the lost city. She gets caught in the path of a bear, and as she attempts to flee, she falls off a ledge, knocking herself unconscious.
A flashback to when Lara was a young girl shows her climbing into her father's study through a window. He tells her that he is going on his greatest adventure yet. He also tells her that she will make a mark on the world and will make him proud. He then moves away to answer the phone.
Lara wakes, heals her wounds and plans to tackle with the bear. Inside its cave is the path to go. Heading back to camp, Lara takes a moment to sleep. Another flashback shows Lord Croft on the phone, arguing with someone. Lara asks him about what is happening and he shouts that they are fools to miss his important discovery.
Present day. Lara is woken up by the sound of gunfire and climbs into a tree to hide, watching a soldier search around her camp. She deals with the enemies and then defeats the bear, following the path inside the cave, reaching an old Soviet Installation. Lara then finds herself face-to-face with a woman aiming a bow at her. The woman tells her that the soldiers had only been in Siberia for a few days and that they had taken some of her people prisoners. She advises her to leave if she wants to live and then disappears whilst Lara is distracted by an explosion. Lara follows the explosion to a Soviet base.
She sees the man that she saw in Syria - Konstantin. He gets a call through the radio, telling him that he has to return to the prison as they have a captive who might know something about the artefact, and he swiftly leaves with Lara following him to a small church, where she overhears Konstantin on the radio to someone who tells him that if the situation there becomes "untenable", they will have to step in. Konstantin reassures him that he will succeed. Two soldiers appear from the sides of the building and knock Lara unconscious.
When she wakes, she is tied to a chair, with Ana captured in front of her. Ana tells her that she doesn't know how she had gotten there and Lara blames herself for not knowing that they'd go after her. Konstantin walks in, places a wire around Ana's throat and partially strangles her. He orders Lara to tell him where the Divine Source is, and she answers that she doesn't know. He then releases Ana who tells him that Lara doesn't know; Lara realises that she is with Trinity. Ana tries to talk her into helping them but Lara refuses and is taken to a prison cell.
Lara starts making her escape. The man in the cell next to her is impressed and asks her if she can get them both out of the cells. She is hesitant at first as she manages to retrieve her weapons but with more persuasion from the prisoner, she eventually agrees to free him. He helps her escape the Gulag, to a courtyard where they overhear Ana and Konstantin talking about moving soldiers to the other side of the mountain to interrogate the natives. Lara stops Jacob from reacting and Konstantin is called away. Lara jumps down to the table and reads their intel before an alarm sounds. They make their escape separately.
They meet again at a railyard. He briefly thanks her for helping him escape the prison before having to evade a search helicopter. It shoots at the bridge's supports, dropping train carriages into the water below. Soldiers surround them so they jump into the water below. Swimming out, cold and alone again, Lara is found by the helicopter. She flees but after a nasty fall, she is again unconscious. She dreams of her young self running into her father's study. She sees him led on the desk, blood dripping over the edge with a smoking gun in his hand.
Lara wakes up inside a cave and Jacob gives her something warm to drink. They talk and Jacob questions her motives. Lara explains about her father and Yamatai, with Jacob asking her if she believes the Divine Source to be real and she answers that if it is, she has to find it and that it needs to be studied as it could make a difference to the world. He tells her that a difference is not always a good thing and questions if she would wish Trinity to have its secret to immortality. She replies with a no and he asks her to alter her path, to help him and his people in repelling Trinity. Then after, she leaves the valley untouched, knowing that she has done the right thing. Lara tells him that while she will help fight Trinity, she will still search for the Divine Source. Jacob stands to leave, to return to his people, suggesting a route for her through the copper mines.
On her way to the Copper Mines, Jacob calls her to tell her that he is pinned down. She decides to help him, and finds him on a bridge, where he saves her from being hurt. They go inside the mines through the mountain, but are separated again when Trinity's soldiers, using large machinery, cause the tunnel to collapse. He tells her to find Sofia and tell her that Trinity are in the mines. Lara continues onwards and soon comes across a large, sealed door. She sees that Trinity's soldiers have already tried to open it with no success, but she manages to get inside, where a large statue of the Prophet stands. On the floor is a mosaic that tells of the Prophet's journey and reveals a map called the 'Atlas'.
Lara enters the Geothermal Valley where she meets the female native again, who was ready to kill her. Lara tells her that she escaped with one of their men, Jacob. When he appears, Sofia is relieved to see her father. He tells Sofia that Trinity is on their way and that they need to prepare, and orders that no harm comes to Lara. The natives light the signal fires and protect the children and elderly, whilst Lara lights a signal fire on a spire. Two of the Remnant and Jacob have been captured and are questioned about the whereabouts of the Divine Source; one man is killed and the other tells him of the map. Lara helps to kill the interrogating soldier and defend the village against the attack.
Konstantin and Ana are in the abandoned church. Noise through the radio tells him that they have been overrun by the natives and Lara. Ana tells him that Trinity won't care about helping her if they have to step in but Konstantin tells her to have faith. He kneels in prayer and asks God to show him the way and his stigmata begins to bleed; he believes that God wants their blood.
Lara joins Jacob whilst he tends to the wounded. He tells her more about the Atlas- an ancient map to the old city- and how Trinity won't find it at the tower. He mentions that his people live in those old ruins and won't be prepared for what is coming, so Lara sets off to help. She soon finds herself at the Acropolis, but there is no one there. Jacob believes that Sofia must have taken them into the catacombs beneath the tower.
She finds them and helps Sofia lead the people to safety. With Trinity converging at the tower, Lara decides to go there. Jacob, through the radio, asks her to get Trinity's attention by attacking the soldiers to lure the helicopter to her position. With the helicopter in range, the natives fire at it to take it down. Sofia talks to her through the radio, saying that they are trapped in the catacombs with Trinity swarming the tower. Lara makes her way there to help. With them taken care of, Jacob arrives and Lara asks him to tell her more about the place. He takes her outside and tells her that his ancestors built Kitezh to protect the Divine Source. When she asks him what it is, he replies that it is an artefact from a time long forgotten, believed to hold a fragment of God's soul. The legend says that those who held the Source were granted immortality. Lara insists that she should get to it first but when he tells her that it isn't her burden, she tells him that she will find it with or without his help. She walks off but is stopped by Sofia, who tells her that the Atlas is in the cathedral, in the archives, but warns her of the Deathless Ones.
Lara reaches the Cathedral but is not alone as Ana and Trinity soldiers are there too. She grabs Ana, putting a gun to her head. With soldiers closing in on them, she wraps her foot in some wire and shoots a lantern. A series of explosives go off and the floor of the cathedral caves in. Ana grabs on to a wooden beam but Lara is hanging upside down. She shoots the generators to remove the weights that are holding her and falls to a ledge below. She proceeds onwards, noticing burnt bodies around her and vessels of Greek Fire, and soon finds the Atlas on a pedestal. She grabs it but Trinity is quickly on her trail. She disposes of them, with some unintentional help from the Deathless Ones, and heads into the location of manufacture of Greek Fire. She uses the explosive barrels to knock over an unstable statue of the Prophet, using it to escape the army of the Deathless Ones. She makes it out alive and returns to the Valley to see Jacob.
She is reunited with Jonah, and Jacob takes them to the Observatory, where the Atlas is placed in a rig and lifted to the ceiling. With the sun light shining through it, it projects a map on the ground. Lara finds out that there is a path to Kitezh under the glacier and the entrance is at the observatory. Jacob knew this all along but before anything more is said, Trinity forces blast their way into the Observatory. Despite their attempts to fight them off, they air lift Jonah and the Atlas away with them. Jacob is injured and Lara tells him that she must go after Jonah.
Trinity have taken Jonah to the weather station. As she makes her way there, she rests inside a carved out tunnel. She dreams about when she visited her father's grave just before heading off to Siberia. When she wakes, she presses on towards to weather station. The scene changes to show Ana and Konstantin using the Atlas. They know where the Divine Source is. Lara heads inside the station and is able to retrieve the Atlas again. On a nearby computer monitor, she sees Konstantin beating and interrogating Jonah and she rushes there, releasing the other prisoners but she is unable to enter the room. Jonah uses her distraction and grabs Konstantin's gun but he doesn't shoot, leaving Konstantin time to take out a knife and stab him. When he leaves, Lara manages to get in. One of the Remnant prisoners tells her that Jonah is dying.
Lara clears the area but Jonah is getting weak, and the Remnants tell her that the only way to save him is to see Jacob. They head to the observatory and Jacob heals Jonah; Lara learning that he is the Prophet. She asks him about the Divine Source, to which he answers that he had found it long ago. He had once used the Source to grant his armies their long lives, however when the enemies attacked, the Deathless Ones brought the ice from the mountain down upon the city, killing thousands. Helicopters fly by in the distance and Jacob says that they will force their way through the ice. Lara mentions the path on the map, but Jacob says that the path, called the Path of the Deathless, is too dangerous. He shows her another path, a tunnel in the middle section of the Observatory steps open up.
She enters a large Orrery, solves its puzzle and continues on. The path has become icy and snowy; Lara is now on the path to Kitezh. The route is dangerous, and she encounters the Deathless Ones again. Reaching the lost city, Lara sees the Chamber of Souls and believes the Source to be there. She presses on, using the trebuchets to destroy the gates. The ice above breaks and Trinity make their way inside. Lara begins to climb her way upwards, tackling the oncoming soldiers, who are also heading towards the Chamber of Souls.
Reaching the top of a nearby building, she sees Ana heading inwards, protected by soldiers, whilst the rest of the soldiers battle with the Deathless Ones. She hears a message from Sofia, telling her to get to cover as she uses a trebuchet to help kill the soldiers. Continuing on and across to another building, the two use the trebuchet shots to take out Trinity's remaining helicopter. It spirals into a large pillar, which collapses and knocks the floor out from under Lara. She falls inside a room where, after taking out the Deathless Ones, Konstantin makes an appearance. He takes away Lara's weapons except for her axes and knife, and she has to outsmart him. Before he dies, Lara tells him that his sister had played him and he tells her that Trinity had killed her father.
With him dead, she rushes to the Chamber of Souls, seeing that Ana has beaten her to the artefact. Lara tells her that her brother is dead and that people are not meant to live forever. A soldier rushes in to tell Ana that they are surrounded and Jacob stabs him from behind. Ana shoots him repeatedly and he falls to the floor. He tells Ana that the Source is not meant for the world but Ana refuses to let it go. The Deathless Ones begin to enter the Chamber and Ana uses the Source. When she falls to the floor and drops the item, Lara picks it up, avoiding looking at it. She looks to Jacob, who nods at her. He knows what she is going to do with it and reassures her that it is okay to do so. She smashes it to the ground. The Deathless army begin to turn to ash. Lara runs to Jacob, who is now dying. She apologises and says that she only wanted to make a difference. As he begins to turn to ash, he tells her that she already has.
Back at Croft Manor, Lara is listening to her father's tapes. Jonah is with her and reminds her that she has a plane to catch. She knows that Trinity is still out there and she believes that she can stop them.
Post credits show Lara and Ana still in Siberia but out of Kitezh. Lara asks her for what she meant by “another Croft doesn't have to die for this”, believing that she killed him, and Ana tells her that Trinity ordered his execution but she couldn't do it because she loved him. She is then shot by a sniper. Over his radio he asks about shooting Lara, to which he is told "not yet".