Rome
Tomb Raider Chronicles begins in the streets of Rome, but before the player moves onto the real game they may complete a detour past an optional training level, set in the backstage of an opera house. The opening sequence shows Lara losing and reclaiming an artefact known as The Mercury Stone, which will be needed if she is to recover the famed Philosopher's Stone. She descends deep into the catacombs of the Colosseum, where she will fight lions and gladiators. The stages in Rome are the easiest in the game.

Russia
During World War II a German U-Boat carrying the legendary Spear of Destiny sank somewhere in the North Atlantic. A Russian crime organization headed by Sergei Mikhailov is out to retrieve it, and towards that end they have bribed a captain of the navy into using his submarine. Lara is closely on their tail. Here she must infiltrate the Zapadnaya Litsa port and sneak on board a nuclear submarine. Underwater the excavation of the wreck is done through an armoured diving suit. The stages in Russia are of an average difficulty.

Ireland
Rumours of demonic activity on the long-abandoned Black Isle has spread across Ireland. Lara, still in her teens, is spending the holidays at Winston's house in a nearby village and Father Patrick Dunstan has arrived to investigate. One night he sets out to travel to the island alone, with Lara hidden in his boat. In these stages, the player must solve puzzles and outsmart enemies without weapons. Lara will be faced with many paranormal creatures such as ghosts, mischievous imps, a sea hag, a talking corpse and the demon knight Verdilet. The stages in Ireland are of hard difficulty.

New York
Lara infiltrates the Head Quarters of Von Croy Industries to retrieve the "Iris", the artefact which was stolen by Werner Von Croy in the Angkor Wat temple many years ago. Assisted by the tech expert Zip, she makes her way through the ventilation system and into the offices of this skyscraper. Some of the enemies the player faces on these levels are indestructible androids. Lara cannot gun them down but there are other ways to dispose of them. The use of stealth is imperative. The stages in Von Croy Industries are the hardest in the game.