The Terris prophesies say that the Hero of Ages will be the savior of mankind, the one who would take the power at the Well of Ascension and give it up, thus saving the world. Vin did not know that Ruin, the entity trapped in the well, could alter any text not written in metal and has been altering the Terris prophesies for centuries.
A year has passed since Vin, the powerful Mistborn who thought she was the Hero of Ages, was tricked into releasing Ruin from the Well of Ascension. Vin was to use the power to change the world, but she gave it up and inadvertently doomed the planet instead. At the well, Vin’s husband, Emperor Elend Venture, was saved and turned into a Mistborn by Preservation, the counterpoint of Ruin.
Now that Ruin has been released, his influence over the world is greater than ever. Earthquakes tear the land apart; ash falls so heavy that it buries the few remaining plants, and the mists appear in the daytime, blocking the sun and killing people. Ruin controls the Inquisitors and the koloss, using them to kill and destroy. Ruin seeks change and for him, change comes through death and destruction. While Ruin wanted to destroy the world instantly when he was released, his power has greatly diminished without his body, which Preservation has hidden. Ruin becomes obsessed with finding his body so he can fully destroy the world.
Emperor Elend struggles to unite what is left of humanity and feed his people by seeking out the storage caches the Lord Ruler left behind in the event Ruin was freed. The caches, filled with food, water and hints on how to fight Ruin, were left in cave systems under various cities across the Final Empire. Vin and Elend hope the final cache in Fadrex City will hold critical information as well as the Lord Ruler’s stash of Atium, which they have been looking for since his death.
Fadrex, ruled by King Yomen, has reverted to a system of skaa oppression. A skaa rebel, Quellion is over Urteau. Fadrex and Urteau are the last two unconquered cities in the Final Empire.
As Vin and Elend travel from cache to cache, the environment grows even more unstable. While they go to Fadrex to open diplomatic relations with Yomen, Sazed tries to do the same in Urteau.
Sazed continues to struggle with his faith, examining old world religions to find one that will explain what happened to his love, Tindwyl, after she died and why so much tragedy has befallen the world. In Urteau, the nobility have been killed, the skaa are free and Quellion rules with increasing violence. When diplomacy fails, Sazed, Breeze and Spook, who was sent to Urteau as a spy, try to secretly take over the city. After being stabbed with a sword, Spook develops strange, new abilities and starts a revolution.
TenSoon returns to his kandra homeland to convince his people that the kandra prophesies regarding the end of the world are coming to pass. He tries to persuade them that they must work with humans to save the world and stop Ruin. Instead, the kandra accuse TenSoon of being a liar and murderer, take the dog bones he has been using and imprison him in a pit. Before being sentenced to death, TenSoon pretends that he found the dog bones degrading, so his captures give them back to him, forcing him to wear them. TenSoon seizes the opportunity and uses the agility and experience he has with the bones to evade his captors and escape from his kandra homeland.
Vin and Elend fail at diplomacy so they decide to take Fadrex City by force. They also discover patterns in the in the mist killings and the secrets of Hemalurgy: the transferring of Allomantic power from one person to another using metal spikes. This is how Ruin creates and controls Inquisitors, the kandra and koloss. The mist is Preservation’s way of revealing Allomancers. While the mist kills some, it makes others sick. When they recover, they discover that they are Mistings: Allomancers who can use one metal. Vin and Elend make observations and plans but they are unable to discuss them out loud for fear of Ruin overhearing.
Vin attempts to break into the cache in Fadrex, but is captured by Yomen, who holds her for ransom. Feeling that he has no choice, Elend uses his Allomancy to control an army of koloss to attack the city, but Ruin shows Elend and Vin that he is ultimately in control when he easily turns the koloss against both Elend’s and Yomen’s armies. Elend and his human army are granted sanctuary inside Fadrex City. Before the koloss attack, Vin escapes, leading the koloss away from Fadrex as she heads toward Luthadel.
In Luthadel, Vin battles Marsh and the last of Ruin’s Inquisitors. She is near death when her earring, a Hemalurgic spike that Ruin influenced Vin’s mother to put there when Vin was a baby, is ripped free. Finally free of Ruin’s influence, Vin absorbs Preservation’s power, destroys much of the city and kills the Inquisitors. Before she can kill Marsh, she ascends as Preservation to join Ruin and watch the world. Vin attempts to fix the devastation that Ruin has leveled on the planet. Filled with power but lacking experience and knowledge, she fails in the same way the Lord Ruler did when he took the power at the Well of Ascension.
TenSoon finds Sazed and takes him back to the kandra homeland, hoping that Sazed will convince his elders that the world is ending. The kandra elders are the original Terrismen who traveled to the Well of Ascension with the Lord Ruler. He gave those men immortality, turning them into shape shifting creatures. The elders accept Sazed’s testimony, and in turn, they tell him about the Terris religion, which centers around their gods Preservation and Ruin. Sazed’s faith is renewed as well as his belief in the Hero of Ages. The kandra also reveal that they have been keeping the Atium, which is Ruin’s body, hidden for centuries.
Elend returns to Luthadel and leads what remains of his people to the kandra homeland, a vast underground network of caves where they can be kept safer from the environment. Elend realizes that his soldiers who suffered from the mist sickness the longest are Atium Mistings, which is Preservation’s plan to provide him with an army of Allomancers.
As Ruin’s massive koloss army attacks, Elend’s small army of Mistings lead a desperate defense. Marsh, controlled by Ruin, faces Elend, and while Vin gives Elend as much supernatural power as she can, Ruin works to block her. Elend realizes he can’t win and makes a final push, but still ends up with an axe in his chest. Dying but victorious, Elend reveals that he and his Atium Mistings used all of Ruin’s body in the battle. Ruin will never have his body and his full power to destroy the world. In a rage, Marsh beheads Elend.
Vin realizes that Preservation gave a part of himself to create humans so people have both Preservation’s and Ruin’s abilities to create and destroy. With Elend dead and nothing left to live for, Vin attacks Ruin, destroying both herself in the form of Preservation and Ruin. While one could never destroy the other, they can both die together.
Sazed, seeing both the bodies of Vin and Ruin fall from the sky, goes to them and understands that he is the Hero of Ages, the savior from the Terris prophecies. He takes both powers and becomes Harmony: Preservation and Ruin in one form.
Using knowledge stored in his metalminds of what the world was like before the Lord Ruler changed it, Harmony fixes the planet. Harmony leaves Spook a note telling him that Vin and Elend are happy where they are.