In 2002, Lara Croft began deciphering the forgotten Tome of Ezekiel, written by a 13th century medieval scholar. She uncovers an artefact that is said to have 'magic' powers - the Black Stone - and she learns that its location is in what was called 'Wolf's Fang Peak', in Sweden. She sets off in search of it, to learn what the meaning of Magic is.
Inside Wolf's Fang Peak, she comes across the tomb of King Heort and realises that he must've used the Black Stone to raise the dead to protect him in the afterlife. Although there are only sketchy details about him in history, she believes that it was this reason that he is only remembered in grim legends and the Tome of Ezekiel. However, there are more than just skeletons guarding the tomb, as a cult called the Teg-Du-Bhorez makes itself known. Lara is intrigued, but as she searches the tomb, she finds nothing except for some symbols. She knows that she has seen them before in the Tome of Ezekiel, so she decides to return home to study them.
The symbols that had Lara found in King's Heort tomb leads her to further investigation of the Tome of Ezekiel. Apparently the Viking King had secretly used the stone to rule his kingdom. Translation of the symbols proves to be a hard task, but finally Lara discovers her new objective. According to the newly deciphered chapter of the book there are two other magic stones, and one is hidden in the temples region of Angkor Wat in Cambodia. Without further delay, Lara heads to Cambodia to search for the stone.
She is looking for the resting place of Surya Varman II, who she believes used the red stone to gain advantages in wars during his reign, and was probably buried with it as well as his treasure. Further inside the temple, Lara overhears a group of Teg-Du-Bhorez members talking about her. They know that she knows about the Black Stone and defeated the apparition guarding Wolf Fang's Peak, and they worry that she'll find out about the Red Stone. They mention about needing all the stones for a final ritual in order for the Teg-Du-Bhorez brotherhood to accomplish its duty. This is useful information for Lara and she presses onwards, finally collecting the Black Stone. She battles with more cultist apparitions and picks up the Red Stone too.
Lara spent many hours deciphering the Tome of Ezekiel, aided by her recent discoveries. She understood that the Tome describes a Prophecy, the Prophecy of Magic. The Prophecy tells that the three Magic stones helped the great conquerors Heort the Viking, Surya Varman II of Cambodia and Marcus Aurelios emperor of Rome. Not having time to completely decipher the whole Prophecy, Lara rushes to the Laconia Island in Southern Italy, where the last stone should be.
In Italy, Lara believes that the last stone is hidden in a villa, where the Tome says that the body of Emperor Marcus Aurelios is buried. She knows that she is on the right track when she finds a group of cultists stood around the White Stone and talking about the prophecy. They are saying that it is time for the Teg-Du-Bhorez to reawaken The Great Grey One through the Third Reunion of the stones. After a battle with them, one cultist appears to tell her that the Third Reunion cannot be prevented. Lara decides that she needs to find their headquarters in order to put a stop to their plans.
Lara goes back to her library in a desperate attempt to discover where the Teg-Du-Bhorez headquarters are located. She finally deciphers the whole Prophecy. 'The First Union gave humans Life. The Second Union gave humans Salvation. The Third Union will give humans Conclusion.' For centuries the Magic stones have been protected by the ancient Secret Society of the Teg-Du-Bhorez. According to the Prophecy of the Tome of Ezekiel the Teg-Du-Bhorez would reawaken their master, the Great Grey One and the Apocalypse would begin. The headquarters is located in a ruined fortress. She sets off immediately.
The place is full of traps and guardians, and after a battle with a cultist, Lara is told that she can only win the fight if she destroys the Great Grey One. She comes across her resting place and places in one of the stones in its receptacle. The Great Grey One wakes up and finds to attack Lara. She battles her as she places in the last two stones, and only then can she defeat her. Soon enough, the fight is over. Defeating the Great Grey One and the Teg-Du-Bhorez secret society, Lara had once again saved the world from destruction. It turns out that the Prophecy of the Tome of Ezekiel foretold of how a mysterious lady would save humanity from a premature, unwanted, conclusion.