The film opens with Croft in an Egyptian tomb, seeking a diamond at one end of a chamber. As she approaches she is attacked by a large robot. After an intense chase and battle, she disables it by ripping out its motivational circuits. She takes the diamond, which is revealed to be a memory card labeled 'Lara's Party Mix,' and inserts it into a laptop computer inside the robot, whereupon it plays music. Now it is revealed that the scene took place in a practice arena in Croft's home, and that her assistant, Bryce, programmed the robot, to challenge her in combat.
It is the day of the first phase of a planetary alignment, culminating in a solar eclipse on the Earth, which happens once every 5,000 years. In Venice, the Illuminati search for a key to rejoin halves of "the triangle," which must be done by the final phase of the alignment. Mr. Powell, an Illuminati member, makes assurances that they are almost ready, but in reality he has no idea where to find the key.
Croft's butler, Hillary, tries to interest her in several projects, but she ignores them. 15 May, as Hillary is aware, is the day that Croft's father disappeared many years earlier. She has not recovered from his loss.
Later that night, Croft has a dream reminding her what her father said about the alignment, and an object linked to it called the Triangle of Light. Waking, she is aware of a clock ticking. Searching for it, she discovers a secret chamber with a carriage clock that had spontaneously begun ticking. Bryce probes it and discovers a strange device hidden inside the clock.
Since the device resembles a clock, Croft consults a clock expert friend of her father's, Mr. Wilson. She believes it is connected to the "Triangle of Light," but Wilson disavows knowledge of the clock or the Triangle. Croft encounters Alex West, a fellow tomb raider with unscrupulous methods. They are attracted to each other, but Croft cannot abide his for-profit attitude. That night, Croft is contacted by Wilson, who tells her that he gave her name to a man named Manfred Powell in regards of the clock. In reality, Wilson is also a member of the Illuminati.
The next day, Croft sees Powell in his home, and shows him photographs of the clock. Later, while discussing it with Bryce, she points out that Powell was lying about his knowledge. That night, armed commandos invade the house and steal the clock despite Croft's attempts to fend them off.
The next morning, Croft receives a letter from her father, arranged to arrive after the beginning of the alignment, where he explains that the clock is the key to retrieve two halves of the mystic Triangle of Light, which is revealed to be an object of phenomenal destructive power that granted its wielder power over time and space. Initially housed in a city built by those who worshipped the object, misuse of the Triangle's power destroyed the city and so it was split into two halves; one was hidden in a tomb in Cambodia, the other half in the ruined city itself, in modern-day Siberia. Her father urges her to find and destroy both halves before the Illuminati can find it.
In Cambodia, West figures out part of the puzzle on how to retrieve the triangle half, but Croft manages to successfully grab the piece and escape the temple after fighting off and destroying a huge six-armed guardian statue.
She and Powell arrange to meet in Venice, since each of them has what the other needs to finish the Triangle. Powell proposes a partnership to find the Triangle, and informs Lara that her father was a member of the Illuminati, which she vehemently denies. Though hesitant at first, she, along with Bryce, meets with Powell for the trip to Siberia. Inside the tomb, there is a giant model of the solar system, which activates as the alignment nears completion. Croft retrieves the last half of the Triangle, but when Powell tries to complete it, the halves will not fuse. He realizes that Croft knows the solution to the puzzle, and kills West in order to persuade her to complete the Triangle to save both West's life and her father's. Croft reluctantly complies, and they then struggle for control of the Triangle, with Croft prevailing.
Croft then finds herself in a strange alternate existence facing her father. He explains that it is a "crossing" of time and space, and urges her to destroy the Triangle instead of using it to save his life. She leaves her father and returns to the chamber, where time is slowly running backwards from the point where Powell killed West. Croft takes the knife he threw into West's chest and reverses it, then destroys the Triangle, which returns time to its normal flow and directs the knife into Powell's shoulder. The chamber begins to self-destruct, Everyone turns to leave, but Powell tells Croft that he killed her father and retrieved his pocket watch with a picture of Lara's mother inside. Croft fights him to retrieve it, killing him and escaping as the chamber comes down around her.
At the mansion, Hillary and Bryce are shocked to see Croft wearing a dress. She goes into the garden to her father's memorial, then returns inside, where Bryce has a reprogrammed SIMON, ready to challenge Croft once again. Hillary reveals a silver tray holding Croft's pistols, which she takes with a smile.