The game begins with Lara setting out on her first expedition about the ship Endurance, with the intention of finding the lost kingdom of Yamatai.
By her suggestion and against Whitman's advice, the expedition ventures
into the Dragon's Triangle, east of Japan. The ship is struck by a
violent storm and split in two, leaving the survivors stranded on an
isolated island. Lara is separated from the others when she is captured
by a strange, savage man and trapped in his cave home. She manages to
escape while her captor is killed as the cave collapses around them. As
Lara tries to locate the other survivors, she finds more evidence that
the island is inhabited, complete with strange carvings, dead bodies,
and ritual sacrifices of animals. She eventually finds her friend Sam
and a man called Mathias, who claims to be one of the passengers. As Sam
tells Mathias the legends of Himiko, Lara falls asleep; when she wakes,
Mathias and Sam are nowhere in sight.
When Lara finally reunites with the other survivors, she and Whitman
decide to break off from the main party and search for Roth, who is
still missing, while the rest of the group (Reyes, Jonah, Alex and Grim)
set out to find Sam and Mathias. As Lara and Whitman explore, they
discover that the island's inhabitants are worshiping Himiko, confirming
that the island is, in fact, Yamatai. Upon discovering a shrine erected
in Himiko's name, they are captured by the islanders and taken to a
settlement along with several other survivors of the Endurance
wreck. When the survivors attempt an escape, the captors turn on them,
hunting them down and killing them. Lara is separated from Whitman and
tries to hide, but is found by Vladimir, one of the leaders of the
inhabitants. Vladimir attacks Lara, but she fights back and is forced to
kill him to save her own life. She fights off the remainder of the
inhabitants as she desperately works her way up the mountainside to meet
up with Roth. Eventually, she locates an injured Roth in a nearby
abandoned village. Using Roth's equipment, Lara sets off for a
communications relay at the very top of the mountain, in hopes of
contacting the outside world and calling for aid.
After successfully hailing a plane that was searching for the Endurance
and setting a signal fire for them to follow, Lara witnesses a fierce
storm materialise out of a clear sky and strike the plane down,
accompanied by a mysterious voice saying "No one leaves" in Japanese.
Feeling responsible for the fate of the pilots, Lara is powerless to
stop the island's inhabitants from killing them. Lara is contacted by
Alex and Reyes, who reveal that Sam has been kidnapped by the island's
inhabitants, a violent cult known as the Solarii Brotherhood. Lara, who
is closest to Sam's position, tries to rescue her, but is foiled by
Mathias, who orders her killed. Lara is saved by the intervention of
strange samurai-like creatures—referred to by the islanders as 'Oni',
demons in Japanese folklore—and taken to an ancient monastery in the
mountains. Escaping again, Lara stumbles onto a ritual chamber, where
she learns that a "fire ritual" was used to choose the Sun Queen's
successor as part of a ceremony called the "Ascension". A terrified Sam
manages to contact Lara and informs her that the Solarii intend to put
her through the fire ritual, which will burn her to death if it is
unsuccessful. Lara makes for the Solarii fortress, with support from
Roth, but as she tries to infiltrate the palace, the Solarii threaten to
murder Grim unless she surrenders. Grim attempts to overpower them, but
is killed in the process. This allows Lara to venture into the palace,
where she witnesses Mathias putting Sam through the fire ritual. Lara
interrupts the ritual by trying to save Sam, but she is overpowered by
Mathias and his men. The ritual continues, but Sam is not harmed by the
flames, which are extinguished by a great gust of wind, marking her as
the rightful successor to the Sun Queen's throne.
Lara narrowly escapes captivity once again and doubles back to help
her friends, whose attempts to reach Sam have resulted in their capture.
Aided by Whitman—who has managed to negotiate some degree of freedom
with the Solarii—Lara returns to the palace to rescue Sam as Roth
commandeers a helicopter to get them out. Having witnessed the storm
that forced the search plane to crash, Lara sends Sam to escape by land
and tries to force the pilot to land as a second storm brews up,
striking the helicopter and forcing them to crash. Lara is nearly killed
in the accident and is revived by Roth. However, Mathias and the
Solarii arrive, and Roth is killed by a tomahawk meant for Lara. While
mourning over Roth, Lara accepts that the storms are not natural, but
are somehow connected to the Sun Queen and designed to prevent anyone
from leaving the island. She meets up with the other survivors, who have
evaded the Solarii long enough to secure a boat and escape the island,
provided that it can be repaired. They are joined by Whitman, who claims
to have escaped, though Lara begins to suspect him of working with the
cultists. Lara and Alex head for the wreck of the Endurance to
salvage the tools needed for Reyes to repair the boat. They find what
they need, but they are attacked by the Solarii and Alex is trapped
under wreckage. Alex decides to trigger an explosion and sacrifice
himself so that Lara can escape with the tools.
Finding an account of a Japanese military expedition to the island
that sought a way to harness the power of the storms as a weapon, Lara
decides to explore an ancient tomb on the coast, where she finds the
remains of a high-ranking samurai who committed seppuku.
It is revealed, in a message he left, that he was the general of the
queen's Stormguard, the Oni that defend the monastery, and that the
Queen's successor took her own life rather than receive the Sun Queen's
power, leaving the Sun Queen trapped in her body after death, and her
rage has manifested in the form of the storms. Lara realises that the
Ascension is not a ceremony to crown a new queen, but rather a ritual
that transfers the original Sun Queen's soul into a new body, and that
the process will destroy the host's soul. Himiko's spirit wants to
escape its current body, and Mathias plans to offer Sam as a new host.
Lara returns to the survivors on the beach to find that Whitman has
betrayed them, abducting Sam and handing her over to Mathias.
Lara, Jonah and Reyes give chase, heading up a river to the
monastery, with Lara arriving just in time to see Whitman killed by the
Oni. After fighting her way through the queen's guards, Lara arrives at
the top of the monastery in time to see Mathias start the Ascension
ritual. She works her way to Mathias, confronting Solarii and guards
alike. Lara kills Mathias when she shoots him from the roof of the
monastery, sending him plunging into the abyss below, before destroying
Himiko's remains to save Sam. With the storms dispersed, Lara, Sam,
Reyes and Jonah leave the island and are picked up by a cargo ship. As
she and her friends sail home, Lara decides that there are many more
myths to be found and resolves to uncover them, stating that she isn't
returning home just yet.
