The Final Empire is ruled over by the god emperor known only as the Lord Ruler. Ash falls from the sky constantly, and mists shroud the world at night. A slave race known as the skaa run plantations and are oppressed viciously by a ruling class of nobility. Vin, a skaa girl, is part of a thief crew. She unknowingly has the abilities of a Mistborn, and thus is able to manipulate all the metals of Allomancy. When she is take into the Ministry to pull off a job, she is identified as an Allomancer by a high ranking Obligator when she attempts to sooth the Obligators emotions.

Meanwhile, Kelsier, another Mistborn skaa, learns of Vin and his powers from a fellow thief. He rescues Vin from an attacking Inquisitor, and brings her into his thieving crew. The crew consists of a Thug named Hammond (or Ham), a Soother named Breeze, a Smoker named Clubs, Dockson (not a Misting, but runs logistics), a Terrisman named Sazed, Yeden (leader of the skaa rebellion) and Kelsier and Vin as the Mistborn. Their goal is to overthrow the Final Empire, and set the skaa rebellion up as the rulers. Kelsier himself will kill the Lord Ruler, if he can.

Kelsier begins to train Vin in the ways of Allomancy, teaching her how each metal works. It soon becomes apparent that Vin is an extremely talented Allomancer, and in spite of her limited training, is nearly able to best Kelsier at times. What seems to be even harder for Vin to learn, however, is how to trust the rest of the crew. Up until this point her life has consisted of nothing but betrayal.

The Job has several key goals: (1) Gather a skaa army of at least 10,000. (2) Get the garrison out of the Luthadel. (3) Destabalize the nobility by creating a house war. (4) Take the palace, claim the Atium, and control the economy of the Final Empire. (5)Get the Lord Ruler out of the city (or kill him if possible). Breeze will use his soothing to aid in recruitment, Ham will work on training the soldiers, Marsh (Kelsier's brother) will become an Obligator and serve as a spy, Kelsier will wreak general havoc among the nobility to start the war, Vin will impersonate a noblewoman to gather information, and Clubs will provide cover via burning Copper.

Vin enters into court as a relative of Renoux, a nobleman who Kelsier controls. Renoux was actually killed and replaced with a Kandra – a form of mistwraith that can consume the body of a man and effectively become that person. At her fist ball Vin meets Elend Venture, the heir to the most powerful House in Luthadel. Over the next few months, she and Elend grow closer despite the warnings from the crew that he is simply showing interest in her to annoy his father.

The army recruitment begins to go well, and Kelsier takes Yeden to the caves where the soldiers are hiding and training. Not long after Kelsier and Ham return to the city, however, they learn that the Yeden has taken the army on a "practice" attack against a nearby city. The attack is successful, but the reinforcements arrive from the Empire, and the army is devastated. Vin and Kelsier arrive to see the remnants of the army being destroyed. When they enter the caves, however, they discover 2,000 men remained behind, believing they were being disloyal to Kelsier by attacking. The remaining men are taken back to Luthadel and hidden throughout the city. Recruitment continues as possible to add to these numbers. On the positive side, the attack did result in the Garrison being dispatched from Luthadel, accomplishing one of the goals the crew needed to overthrow the city.

On a whim, Kelsier and Vin travel to the palace to investigate a room that the Lord Ruler enters every few days. Kelsier believes it holds the secret to defeating him. They fight their way to the inner chamber, but when they arrive 3 inquisitors are waiting for them. One goes after Kelsier, but 2 attack Vin. She attempts to escape, grabbing a book in her defense, but is stabbed in the side. Just when she is about to be taken, Sazed arrives and is able to fight off an Inquisitor and take Vin home. It takes her a long time to recover. Meanwhile, Sazed begins translating the book Vin found, which appears to be a logbook of the Lord Ruler when he was simply a man on a journey to save the world from the Deepness.

As the book is translated, Vin learns much. In particular, she discovers Sazed is a Feruchemist, which means he can store up abilities in metal. This is how he stores memories, as well as the strength he used to rescue Vin from the Inquisitor. Unfortunately, there is no information on how to defeat the Lord Ruler or on the Eleventh Metal, something Kelsier believes holds the secret to defeating the tyrant, but which he can't figure out how to use.

Marsh succeeds in infiltrating the Obligators, and finds success thanks to his ability as a Seeker. He sends information to Kelsier about how the Ministry has Soothers throughout the city who work to keep the skaa's emotions beaten down in order to prevent rebellion. One night, Kelsier and Vin go to meet Marsh, but find his body destroyed and a hidden note about how the Inquisitors were showing interest in him and that they may be onto him. Devastated, Kelsier heads to the Pits of Hatshin, where Atium is mined. He kills the guards, releases the prisoners, and proceeds to destroy all the Atium crystals, meaning no Atium will be produced for several hundred years.

Meanwhile, Elend discovers that Vin is lying to him, and he believes she is a spy for another house. He rejects her, telling her they cannot be together. Vin, however, soon discovers that Elend is going to be assassinated that night. She goes to his room (via the roof) and discovers 2 Mistborn and other Mistings about to kill Elend. He fights them off, killing one Mistborn in the process and saving Elend's life, though he doesn't realize it was her, or what danger he was in. Soon, however, he learns that she was, in fact, a skaa thief, and not a noble spy. Strangely, this is good news to him.

Renoux and his house are captured and brought to the city for execution. Kelsier tries to free them, but is attacked by an Inquisitor. A battle ensues, and Kelsier is able to kill the creature by beheading it. However, the Lord Ruler arrives and Kelsier allows himself to be killed without a fight. That night, the skaa rebel, the soothing stations are destroyed, and the invasion of the palace begins. Vin decides that she must kill the Lord Ruler if there is any chance for success. She yet again invades the palace in search of the inner chamber. She makes it inside, only to find the Lord Ruler (now looking very old) sitting in the room. She burns the Eleventh Metal, but it only serves to show the past self of anyone she looks at.

Vin is captured by the Inquisitors, but not killed. Instead she is taken before the Lord Ruler and the leader of the Obligators. She is his daughter, and when this truth is revealed the Lord Ruler has him killed, and instates the Inquisitors as the head of the Ministry. Vin is taken back to her prison cell for torture and interrogation. The Inquisitors leave, however, for the ceremony that will place them in charge of the Ministry. Sazed, looking beaten and tired, is thrown into a cell next to her. They will torture him to punish Vin. However, Sazed uses stored strength from metals he swallowed to free himself and Vin. Vin finds her items, and replenishes her metal supply just as Elend arrives looking for her. She fights off the human guards, and tells Sazed to leave with Elend. She goes to the Lord Rulers throne room believing she knows how to kill him.

When she arrives, she burns the Eleventh Metal and attempts to attack the past self of the Lord Ruler, but nothing happens. An Inquisitor begins to choke her to death, but suddenly he is killed by another Inquisitor. It turns out Marsh was not killed, but was turned into an Inquisitor. He killed all the others nearby, leaving only Vin and himself with the Lord Ruler. He attacks the emperor, but is not able to hurt him. Vin is nearly dead when she notices that the past self of the Lord Ruler is not a human man, but a Terrisman. She Pulls as hard as she can and pulls out the 2 bracelets the Lord Ruler had embedded in his arms. They were, she realized, the source of his power as a Feruchemist. His body begins to decay rapidly without the youth stored inside the bracelets. Vin approaches him and stabs him through the heart with a spear, killing him, but not before he could claim that by destroying him, they were only dooming themselves.

Elend is set up as the new King, and he brokers peace between the skaa, the ministry, and the nobles. Vin goes to him in the night, and they hug.