Lara Croft, along with a team, are on board the Endurance, sailing to a location in the Dragon's Triangle, hoping to find the lost kingdom of Yamatai. Suddenly, the research vessel is caught in a violent storm, breaking the ship into two. The survivors make it onto a nearby beach, but Lara is separated from the team and captured. Whilst trying to escape a cave, she causes an explosion, of which the failing debris kills her captor. She crawls out into the open air - it is now daylight and she can see the extent of the storm as well as the land she is on.
Lara immediately sets out to find her friends, coming across other inhabitants who are hostile. Eventually she finds Sam Nishimura talking to a strange man called Mathias, who says that he is a teacher. He seems interested in what Sam has to say about Himiko. Lara falls asleep and when she wakes, she finds that Sam and Mathias have gone. She panics and when she tries to go in search for them, her foot gets caught in a bear trap. After fending off wolves, some of her group find her - Reyes, Jonah, Whitman, Alex and Grim. They split into two groups: Lara and Whitman go off to find Roth whilst the rest go off to find Sam. The pair stumble upon a shrine dedicated to Himiko, showing that there are people who still worship her; however they are ambushed. Lara wants to try and resist them but Whitman hands themselves over and they are captured by the other inhabitants.
They are taken to an area where other Endurance survivors are being held at gunpoint. They try to escape but the inhabitants kill them. Lara tries to hide from the group's leader, Vlad, but he finds her and she is forced to kill him. She is horrified by her action, her first human kill, but soon realises that she has to kill or be killed. She manages to find Conrad Roth fighting off a pack of wolves. They have attacked his leg and she has to get supplies from the pack that they took to their den to patch him up. Returning with the pack a short while later, Roth tells her that they need to send out an SOS via a nearby communication tower and that Lara has to go and do it. Nervously, she goes but soon learns that the communication panel at the radio tower is broken and the only other option is to climb up the tower. Courageously, she climbs the extreme height and uses the panel at the top to send out a Mayday signal. The plane N177A responds, saying that they had picked up the SOS that Roth had sent out before the Endurance was shipwrecked. However, after creating a marker for it, the plane is struck by lightning in a sudden storm. A Japanese voice rumbles with the storm "no one leave". The pilot is killed so Lara goes off to try and help the co-pilot. However he is killed too.
Lara is then contacted by Reyes and Alex who tells her that Sam has been captured by the islanders, a group who call themselves the Solarii, followers of Mathias, worshippers of the Sun Queen. Lara attempts to save her but Mathias orders for her to be killed, however she is saved when a large Oni Stalker storms through the area, taking out a few of the Solarii. After escaping, Lara is contacted by Sam who has taken a radio from one of the guards. She says that she is going to be put through a fire ritual. Lara vows to find her, and along the way, she finds Grim. The Solarii try to take him hostage, using him as leverage to get Lara to disarm herself and but Grim doesn't allow her to give up the fight; he takes them out, sacrificing his own life in the process. Lara presses on, hoping to make his sacrifice count, and with Roth's help in getting across the bridge safely (via his usage of a sniper rifle and commands), she heads inside a fortress where the ritual is beginning. Sam is tied to a wooden pole and Lara is held back as the fire is lit but a strong wind blows the fire out and Mathias believes that this means that Sam has been chosen to be the next Sun Queen. Lara escapes the Solarii's clutches and finds Reyes, Jonah and Alex suspended in a cage in the ceiling of a geothermal cavern. She helps them to leave before she continues on. She finds Whitman and then Sam, and helps her to escape. Outside, Roth has climbed aboard a helicopter and tries to help Lara to leave the island. Lara refuses to leave without the others and orders the pilot to land, but a storm brews, preventing them from leaving the island and thus causing the helicopter to crash. Lara is unconscious on the ground and Roth manages to revive her. She is still weak as he fights off Solarii. Mathias throws an axe in Lara's direction, and as he is out of ammo in the pistol that he is holding, Roth turns his back to it, the axe embedding itself into him. He falls to the ground; Lara is conscious enough to say a few words to him before he dies. The rest of the group find them and they give Roth a warrior’s send off. Lara realises that somehow the Sun Queen is connected to the storms and that it won't allow them to leave. Reyes mentioned that she has found an old PT boat on the beach that she will fix so that they can escape the island.
Lara plans to take the boat inland to go and visit the burial chamber. She joins the others on the beach and soon after, Whitman shows up, claiming to have been chased by the Solarii. Lara doesn't trust him but she decides to go and find Alex, who went to the Endurance to collect some tools. The Solarii are there also, and Alex has gotten his leg stuck. He sacrifices his life for Lara so that she can have a head start off the wreck with the tools. Escaping just before one half sinks into the water, she soon finds old log books and a wartime document that show that scientists found the tomb of an important General in the cliffs. After returning back to the beach, Lara explores the tomb and finds the body of the General. He committed seppuku, but inside the butt of his sword is a message. It said that he had failed his Queen, the ritual was corrupt, and that the Sun Queen was now living a half life: her soul was trapped in a decaying body. Her rage was in the storms and she would not stop while her soul was tied to the earth. Lara realises that in order to stop the storms so that they can leave the island, she needs to destroy the Queen's body in the ritual chamber.
She returns back to the beach to update the rest of the crew but learns that Dr. Whitman has taken Sam and plans to hand her over to Mathias. Lara tells the others her plan of using their boat and destroying the Queen's decaying body and they follow the river up to the monastery. Whitman is killed by the Stormguard whilst Mathias takes Sam to the top of the monastery. When Lara arrives there too, Mathias has already begun the Ascension Ritual. Lara battles the Solarii and then Mathias himself. She shoots at him until he falls over the rock edge and then she stabs Himiko's body with her fire torch. The Sun Queen screams and her body explodes, breaking the cycle of the transference of souls and setting the Queen's soul free. Sam has been saved; the dark clouds fade away as the sun light pours through. Lara carries Sam back down to the boat and they can finally leave the island.
Lara flicks through her notebook, realising that even the craziest myth could hold some truths. She decides that she isn't going to return home yet.