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The game opens by telling of Garrett as a youth living on the streets of The City. One evening he tries to pickpocket a strange man standing in an alley, who catches Garrett in the act. He is a Keeper and the fact that Garrett can see him at all is unusual. The man offers to take Garrett in and show him the Keeper ways. Garrett accepts and enters into Keeper education for some time, but instead of staying with the Keepers, Garrett leaves to put his skills to other uses (The Keeper Annals state that Garrett left out of the "folly of anger". The nature of this anger is not explained).
Some time later Garrett is working as an independent thief in the City. He steals an expensive scepter from a noble, breaks into the Hammerite prison to spring his fence (who dies while still in prison) and ventures deep into the catacombs looking for treasure. Shortly after this thugs working for the local Warden, Ramirez, attempt to kill Garrett for non payment of tribute. Garrett turns the tables, escaping and going on to humiliate Ramirez by looting his mansion. This brazen display of skill attracts the attention of Viktoria, a somewhat mysterious independent fence. She contracts Garrett to steal a magical sword from the eccentric nobleman Constantine. Upon successfully returning from Constantine's bizarre mansion Viktoria reveals that she and Constantine are old associates who were testing Garrett. Constantine offers Garrett a fortune for the job of retrieving the gemstone known as The Eye. Getting to The Eye means Garrett must venture through the abandoned and walled-off Old Quarter of the City to the old Hammerite cathedral. A mysterious catastrophe, rumored to involve great fires and many undead, caused the area's abandonment decades ago. Garrett finds the cathedral sealed, but the Eye itself tells him of an old Keeper library hidden nearby. Writings there tell of where the talismans that open the cathedral are hidden and how the Keepers almost revealed themselves in order to assist the Hammerites in containing a great evil. The first pair of talismans are found in a place called The Lost City, the ruins of an ancient civilization buried beneath the existing city, its entrance hidden by the Keepers. To get the second pair of talismans Garrett enters a Hammerite temple in disguise. Successful, he then returns to the cathedral and collects The Eye from amid the many undead, escaping with the help of Hammerite Brother Murus' ghost.
Garrett visits Constantine to hand over The Eye and collect his payment. Instead of paying, however, Constantine reveals himself to be the fabled Trickster (aka The Woodsie Lord), the entity worshiped by the Pagans, and Viktoria, his consort. They bind Garrett in vines and pluck out one of his eyes, using it to seemingly activate The Eye stone, and leave him for dead. Some time later two Keepers find and free the unconscious Garrett from the vines. The Keepers then leave Garrett to escape by himself through the caverns beneath Constantine's mansion and amongst some new and strange beasts. Once he reaches the surface Garrett decides the only thing to do is visit the Hammerites and tell them about what has happened. He heads for the temple but discovers that the Trickster's minions have gotten there first. Venturing inside he finds the remaining Hammerites in a hidden sanctuary down in an underground cavern. With stealth being the only hope against the Trickster's army, the Hammerites provide Garrett with a booby-trapped copy of The Eye. Garrett descends into the Trickster's realm, where he finds the Woodsie Lord performing a ceremony with the Eye. Garrett stealthily swaps the Eye for its trapped copy, which then explodes, thus striking down the Trickster as he attempts to finish the ceremony.
The coda shows Garrett walking back to town alone through the snow. Life appears to be returning to normal. A Keeper approaches. The two converse and The Keeper warns Garrett, telling him of a book he should read. Close observation reveals Garrett now has a mechanical eye. Garrett rejects Keeper 'help' in his life and says to tell the other Keepers that "I'm through. Tell them Garrett is done". He then walks away into the city streets. The Keeper says quietly "I will tell them this: Nothing is changed. All is as it was written. The Trickster is dead. Beware the dawn of the metal age.", foreshadowing the sequel, Thief II: The Metal Age.
