The story begins with a voice over from Richard Croft, telling the history of Himiko and of Yamatai. In present day, Lara is training in a boxing gym in London. She is unable to win and has to tap out. She changes her clothes for her job as a food courier. She overhears two men talking about a fox hunt, a street bike racing game, but they need a fox. Lara volunteers to do it for £600. They take to the streets and Lara sets off, with her courier job and knowledge of London coming to good use for when she avoids her chasers. She loses concentration for a split second, believing that she sees her father walking along the footpath. She swerves to avoid a driver climbing out his car and crashes into a Police car, where she ends up being arrested.
Ana Miller, her legal guardian, collects her from the Police station, questioning her on her actions. Lara says that she needs the money but Ana reminds her that she has a trust fund ready for her if she would only sign the legal documents agreeing that her father, Richard Croft, is dead. At night, Lara reminisces about her father handing her a jade necklace.
The next day, Lara heads into Croft Holdings to meet Ana, but the receptionist mistakes her as a standard courier. After correcting him, she sits down with Ana Miller and family solicitor Mr Yaffa to sign the necessary papers. Lara sees him looking at a Karakuri, a Japanese puzzle. She is able to solve it within seconds, accessing a hidden photograph of a young Lara with her father, a key and a scrap of paper that read: 'The first letter from my final destination'. Lara doesn't sign the papers but returns to Croft Manor, visiting the family crypt. Richard was not interred here as his body was never found, but there is a space for him. She presses the letter R and reveals a keyhole, and using the key, a section in the wall opens up and a stairway makes itself known. This leads to a hidden room under the crypt, more specifically, Richard's hidden study. He was paranoid about a group called 'Trinity' finding his research on Yamatai and Himiko. In his video message on a camcorder, he asks her to burn all of his research on Himiko. Rather than burning it, Lara learns all she can from it, even finding the name of a captain who was willing to sail to the Dragon's Triangle.
Lara then heads to a Pawn shop, selling her Jade necklace to raise funds for the journey. It is sold for £8000. She heads to Hong Kong to find the Captain, Lu Ren, but she runs into a bit of trouble; her bag gets stolen by street thugs. A chase begins and she gets her bag back by using her knowledge of self defense. One wields a knife and she runs, stumbling upon the Endurance. The captain is a little drunk and points a shotgun at them, scaring off the thugs. He threatens Lara but he passes out. Lara takes him into his boat, placing him in the shower and sprays him with water until he wakes. She explains that her father bought a boat from Lu Ren, but Lu says that actually, her father bought the boat from his father, who is also missing. Lara tells him that she knows where they both should be, and they find the co-ordinates for an island in the middle of the Devil's Sea on a map. She bribes him to captain the boat.
They travel for days, Lara continuing to solve a Karakuri from her father's study, until the seas become choppy and the weather becomes stormy. Lu says that they have made it to the Devil's Sea. The boat crashes and the two are thrown overboard. Lara washes up onto a beach but is knocked unconscious. When she wakes, she is in a tent with a man who appeared to be friendly at first. He knows her name and asks her why she is on the island. He introduces himself as Mathias Vogel and gives her a can of peaches. He has been on the island for 7 years but he cannot leave to see his two daughters until he has completed his task on the island. He lets on that he has read her research and that he shot her father a couple of years ago for not cooperating. She heads outside to get some air but a mercenary pushes her along a path, even tying her hands together. She sees poor, tired workers, even spotting Lu again. Mathias sends the orders to pack up the equipment as they are now moving camp due to her research.
Lara walks with Lu as they carry bags along a path. They talk of what is happening, Lara tells him that her father was killed and Lu explains that the workers informed him of his father being killed in cold blood also. Mathias spots the blocked entrance to Himiko's tomb and the workers unpack. Lara and Lu see a worker suffering but despite Lara and Lu pleaing with a mercanary to give the worker rest, Mathias kills him outright before aiming the gun at Lara. He panics her but then drops the gun. It is here that they come up with a plan to get Lara to escape. Lu attacks a mercenary, which draws their attention and Lara escapes, but just barely. Lu is shot in the shoulder whilst Lara tries to cross a fallen tree across a gap. She falls into the river though, following the current.
She sees a drop coming her way and scrambles to save herself, only managing to grab an extruding part of an aeroplane wing that was hidden at first glance. She climbs up, feeling the wing about to break, and charges towards the body of the plane. There, she climbs in and frees her hands. The plane is now also slipping but she is unable to escape it, instead, landing upon the glass window. It cracks but she spots a parachute. She grabs it and puts it on just in time to sail through the air and into the forest. She crash lands and sees that a shard of wood has pierced through her body in her right hip. She grits her teeth and removes it, and she slowly stands to see a beach in front of her, covered in wrecks of old vessels. She stays until night time but creeks in the surrounding jungle wake her. A mercenary has found her and tries to apprehend her but Lara kills him, drowning him in a puddle of water, making this her first kill. Before she can truly think of what she has done, she sees a figure in the woods and she gives chase. She follows the man into a high cave only to discover that the man is her father. Richard believes that he is seeing an apparition but Lara persuades him otherwise. He tends to her wound and Lara sleeps for the night.
In the morning, Mathias is making breakthroughs with finding the entrance of Himiko's tomb. Lara meanwhile wakes up only to find herself alone. She panics but finds her father outside, tidying himself up. He asks about her life but Lara tells him that she didn't go to any university. He talks about Himiko and his attempts to leave the island but he stayed to stop Mathias from finding Himiko. Lara has to admit that she did not burn his research like he had asked and gets told off by her father, who had spent years creating decoys and fake clues. They have a difference of opinions: upon keeping the tomb hidden, Richard believed that Lara would be safe and the world would be safe. Lara believed that the research helped her find her father and that they now needed to get off the island. Unhappy with this, Lara grabs his bow and arrows and takes it upon herself to take on the mercenaries.
Mathias is struggling to open the tomb, it is guarded by wheels similar to a Karakuri puzzle but he cannot work it out. Lara kills a mercenary guarding Lu Ren and the workers. Her plan is to get the satellite phone that Mathias has. Lara and Lu Ren take on any of the mercenaries that bother them; Lara causes a distraction and Lu takes the workers to safety. He vouches to return back to help Lara. She grabs the phone from Mathias' tent and is ready to leave, but she sees her father admiring the tomb entrance. Mathias creeps up on him and forces Lara to then solve the puzzle or else he would kill Richard. Despite Richard's plea, Lara does as he asks.
They enter in, quickly realising that the tomb is heavily guarded. Richard tells them that the traps are designed to keep people inside the tomb, to stop them from fleeing. Lara slowly crosses a Chasm of Souls and begins to impress her father. They continue onwards but one of the mercs trigger a trap; the chamber is sealed off and the floor begins to crumble and fall. Lara notices a key hole and Richard, Mathias and the mercs scramble to find semi transparent keys. It is a colour puzzle; the blue and yellow keys make green, the colour of life. The door finally opens and they continue onwards. They see the bodies of Himiko's army, one thousand Hand Maidens who sacrificed themselves to serve her in the afterlife.
They light up the tomb chamber and the mercenaries remove the lid off the sarcophagus. Lara and Richard watch on in fear as the well preserved body of Himiko is revealed, only for it to start deteriating when the corpse reacts with oxygen. Lara realises that Himiko actually sacrificed herself to save her people, protecting the world from the disease that she carried. The body sits up, a trick to scare people. Mathias' right hand man, Lieutenant, touches the body but very quickly becomes infected. The others stand and can only watch on as the merc's skin turns grey, infecting his brain and turning him crazy. Mathias has no choice but to kill him. Richard pleads with him to leave it here, but Mathias wants to go home, so he takes Himiko's finger. Lara and Richard fight back; Lara using one of the tomb's traps against the last merc. Richard and Mathias are in a stalemate during a gun fight but Richard is attacked by an infected merc who came back to life. He is left with no choice but to touch him to defend himself, but he ties his belt around his arm to try and stop the spread of the infection. Lara returns back to her father, Mathias took off when Richard was distracted. He tells her that he is infected and that she needs to go and stop Mathias from getting out of the tomb. Lara realises that her father is going to kill himself and is distraught that she has to once and for all lose him. Lara says goodbye and goes. Richard uses Trinity's detonation charges to destroy the chamber, Himiko's body, as well as kill himself. Lara catches Mathias upon the ladder bridge crossing the Chasm of Souls and they fight a gritty battle, where Lara kicks the ladder down into the pit. When he is weakened, she grabs the bagged finger of Himiko and jams it into his mouth. He is now infected with the disease so she kicks him down into the chasm. The tomb is beginning to crumble so she uses the climbing axe to aide in her escape. She reaches the surface, where Lu Ren and the workers are searching for her. She realises what has happened and what she has lost. A Trinity helicopter fly over and they commandeer it.
Back in London, some time later, Lara signs the documents, legally declaring the death of her father, with Ana as witness. She is now in charge of Croft Holdings, putting Ana in charge of the running of it. Lara talks to Mr Yaffa whilst studying the list of incomes and outgoings, she realises that they run a lot of companies, including one familiar company, Patna Ltd. She returned back to her father's study and sees her father's research into Trinity and Patna. She realised that Ana had some play in Patna and that she was a traitor to her family.
Lara returns back to the Pawn shop and buys back her necklace. She looks up and spots some guns in the back room. She picks up a H&K 9mm. The pawn shop wife asks if she likes that one, and Lara picks up two.