This synopsis will contain spoilers!
A year has passed since the Lord Rulers death at the hands of Vin. She has become a legend, and the living icon of the Church of the Survivor, which has begun to grow up around Kelsiers sacrifice and preaching during the previous book. Elend, now the King of Luthadel, struggles to keep control of the city in the face of 2 invading armies – his father and Lord Cett. The two armies besiege Luthadel, and Vin must burn metals night and day to protect Elend from attempted assassinations.
Vin tells her Kandra, OreSeur, to take the shape of a wolfhound to hide his identity and allow him to keep up with her during their nightly patrols. Additional bones are discovered in the palace, however, and it becomes apparent that there is a Kandra spy in their midst. Despite their initial rocky relationship, Vin and OreSeur grow progressively closer throughout the book.
Vins patrols consist of watching out for a ghost in the Mist, a powerful thumping (which she realizes could only be coming from the Well of Ascension), and encounters with Zane, Straff Ventures own Mistborn. Zane is insane, but Vin does not realize it and becomes somewhat enamored by his talk of freedom from being told what to do and being used by others. He is Elends half-brother, though Vin and Elend do not know it. He believes he hears the voice of God, who tells him to kill everyone he sees, except for Vin.
Meanwhile, a Terriswoman named Tindwyl arrives in order to teach Elend how to become a better king. She treats him harshly, but as a result is able to shape Elend into a more confident and better leader. Once her job is complete, she begins to help Sazed as they research the legend of the Hero of Ages. Many things that they learn bother than, and seem inconsistent, but they are not sure why that is until one night, when the Mist spirit arrives and is able to indicate that something was causing written words to be changed. The legends they studied, therefore, were slightly manipulated.
A third army, this time a group of monstrous creatures called Kolloss, join in on the siege. Vin, while attempting to discover the Kandra spy, learns more about the Kandra people. First, they cannot burn metals, so anyone burning metals is not the Kandra. Second, if she uses duralumin while pushing on a Kandras emotions, she can take complete control of the creature.
Despite his more confident stature, Elend is voted out of his position as King by the parliament he set up. Instead, Lord Penrod is made King. As the situation gets worse, the decision is made to send Vin, Elend, and Spook off on a ruse meant to keep them safe during the inevitable attack. They leave, but Vin, realizing something is wrong, turns back. She arrives and is able to fight off the invading Kolloss. Sazed fights valiantly, but Tindwyl is killed, devastating Sazed. However, the tide is truly turned when she remembers something OreSeur had said about the Kolloss being cousins to the Kandra, and is able to take control of them as well. This ends the fighting with the Kolloss, though Straff Venture still remains camped outside the city.
There is a final battle against Vin and Zane when she refuses to go off with him, deciding instead to remain loyal to Elend. During this fight she discovers that OreSeur was actually a Kandra named TenSoon, and had been the spy all along, having killed the original Kandra months before. Despite his contract with Zane, however, he reminds Vin she can control him at a crucial moment, allowing her to save herself from a death blow. Zane, however, burns Atium (which Vin no longer has), and the fight looks to be over, when Vin realizes that she can discover what SHE will do, by watch the way Zane is reacting (since he will see her future). She does so, and is able to react with perfect time to defeat Zane.
Vin, wounded, returns and has Sazed marry her and Elend. Vin kills Straff, and is able to establish a truce, with Elend as the emperor. With Sazeds help, she realizes the Well of Ascension is now in Luthadel, and she goes there with Elend and Sazed. They must fight off an Inquisitor, which they do. At the Well, the Mist spirit stabs Elend, but Vin releases the power, even though she knows doing so will mean Elends death.
They were wrong, however, and as a result they release Ruin, the force of destruction that the Well of Ascension was keeping imprisoned. The Mist spirit was actually trying to help by stabbing Elend and trying to force Vin to use the power instead of releasing it. Still dying, the Mist spirit has Vin give Elend a strange metal which, by consuming, turns Elend into a Mistborn.
Vin and Elend realize they must now attempt to combat the destructive power that The Lord Ruler had been holding back for the last thousand years.