The story begins in Paris where a serial killer the press have named "The Monstrum" has been terrorizing the city, killing over seventeen seemingly unconnected individuals in a brutal, ritualistic fashion. Accused of the murder of her one-time mentor, Werner Von Croy, Lara is forced into hiding. Following notes written in a journal by Von Croy, Lara races to recover five hidden paintings before a secret organisation called the Cabal, whose ultimate goal is world domination and immortality with the assistance of an ancient biblical race known as the Nephilim. Through her adventures, Lara is first hindered then helped by Kurtis Trent, the last surviving member of an order that splintered off of the Knights Templar in the 15th century called the Lux Veritatis (Latin for 'Light of Truth'). Near the end of the game, Kurtis is seriously wounded by the mutant creation of a Cabal scientist, but there are indications that he did not actually die.
Pieter Van Eckhardt is the main antagonist. A normal 15th century alchemist, he was contacted by an extinct race known as the Nephilim (the product of relationships held between fallen angels and humans) and entered a blood pact with them in exchange for immortality, and was tasked with the creation of a powerful weapon known as the Sanglyph (literally 'blood-sign'), able to utilise human blood and body parts to resurrect the Nephilim if it would ever become necessary. To keep the Sanglyph safe, Eckhardt split it into five pieces and hid each piece behind five paintings he created depicting evil imagery.
As time went on, Eckhardt grew ever more evil and powerful, and eventually formed a group known as the Cabal, four individuals who all shared the same desire for immortality. To attain this immortality, the Cabal prepared to resurrect the Nephilim. Eckhardt believed that by using the Nephilim he would attain immortality and dominate over all. However, a group of Christian monks known as the Lux Veritatis was formed and were able to stop Eckhardt's plans. The Lux Veritatis acquired three ancient weapons of light called the Periapt Shards, led by Brother Obscura, they used them to seal Eckhardt in a deep containment pit near their headquarters, Castle Kreigler located near a palace in Germany. The seal on Eckhardt would only last if the three Periapt shards were combined. Brother Obscura took the five paintings that contained the pieces of the Sanglyph, and painted over the previous images of evil with new religious images. These were hidden throughout Europe in locations known only to the Lux Veritatis, and were christened the Obscura Paintings. He secretly made copies of each, referred to as the Obscura Engravings, with each engraving containing an encoded map to the location of the original painting.
Before the main game story starts, before the end of the second World War in 1945, Castle Kreigler was bombed, causing one of the shards to separate from the other two. Eckhardt escaped the pit and vowed revenge against the Lux Veritatis, he then revived the Cabal basing it out of Prague. The new Cabal became devoted to hunting down any members of the Lux Veritatis. Eckhardt also managed to obtain the third Periapt Shard from the Lux Veritatis. He hid these shards in his old laboratory, deep underground beneath the Strahov, the headquarters of the Cabal. Eckhardt and the Cabal set out to reclaim the five Obscura paintings, in order to acquire the Sanglyph. By the time Lara became involved, the Cabal had already attained three of the five paintings. Eckhardt then hired Werner Von Croy to find the last two. Von Croy did learn of the location of the fourth painting beneath the Louvre from the Obscura engravings, but never informed Eckhardt because he learned of Eckhardt's evil plans to use the paintings. Von Croy then asked for Lara Croft to assist in finding the paintings, shortly before he was murdered.
The Sanglyph, whose five pieces are hidden behind the Obscura paintings in various guarded temples, are infused with dark Alchemical powers and give the bearer immense powers in the realm of Black Magic. Lara finds the two remaining paintings in Paris and Prague, though Eckhardt takes them from her before retreating to his old laboratory, where he starts reviving the Nephilim race. The Cabal had retrieved the last Nephilim specimen from Turkey: a Nephili body which had been named "the Sleeper" (it is also called the Cubiciulum Nephili by the Cabal).
During the final confrontation with Lara, Eckhardt starts the process of reviving the Sleeper, using the blood of the Monstrum victims. He battles Lara using the Sanglyph, but he is eventually killed by Karel, his right-hand man, who stabs him with the third Periapt Shard. Karel reveals himself to be the last surviving Nephili and that all the people who have helped Lara died at his hands to avoid the destruction of the Sleeper.He also unwittingly reveals that it was he that murdered Von Croy in the shape of Eckhardt (thus revealing that the Nephilim are shape-shifters) and spared Lara because Von Croy said she would be of great assistance in obtaining the paintings. He then offers Lara a chance to join him in his resurrection. Lara, disgusted with his callous attitude to human life and Von Croy's murder, refuses, and decides to put an end to it by using the Sanglyph on the Sleeper thus overloading it with the new blood the Sanglyph has collected, destroying both it and Karel.
