Clash of Kings picks up the story where it ended in Game of Thrones, the main focus being on the civil war in Westeros. At the same time, events happening behind the Wall and in the distant east are recalled.
Behind the Wall, Lord Commander Jeor Mormont with a large group of Brothers from the Night’s Watch go deeper into the haunted forest discovering villages abandoned by wildlings. They stop at Craster's Keep, a friend of the Watch that tells them that Mance Rayder, the King Beyond the Wall is gathering all the wildlings.
The party leaves and goes deeper into the woods until they reach a ruined fortress known as the Fist of the First Men. There, Jeor Mormont decides to send a small group of Brothers to scout the Skirling Pass. Qhorin Halfhand is chosen to lead the party and he chooses Jon Snow to go with him.
They discover wildling activity in the mountains and they soon realize that they are followed by a group of wildlings. Qhorin orders Jon to infiltrate the wildlings to find more about their plans. In order to be more convincing, Jon kills Qhorin and then he is reluctantly allowed to join the small group of wildlings after a wildling girl, Ygritte agrees to speak on Jon’s behalf to Mance Rayder. It is from her that Jon finds that Mance is not going further North, but rather advancing towards the Wall with an army in the tens of thousands.
In the East, Daenerys travels through the res waste with a fraction of the members of her husband’s khalasar. Some of the members from Daenerys ’khalasar die as a result of the harsh conditions they have to go through. They stop in an abandoned city while Daenerys’ bloodriders are sent to scout the surroundings. After a few days, one of them returns with a welcoming party from the city of Qarth. Daenerys tries to find someone willing to help her regain her throne and even tries to form an allegiance with warlocks.
Her efforts are useless as she doesn’t find the help she needs. She is convinced to return to the Free Cities after an assassin is hired to kill Daenerys. She is saved by two men who claimed to be sent by Illyrio Mopatis. Daenerys agrees to return with them to the Free Cities.
In the Seven Kingdoms, the civil war complicates further more.
Theon Greyjoy is sent back to the Iron Islands by Robb Stark in the hope of securing an allegiance between them. The head of house Greyjoy refuses to accept Robb’s terms and starts a campaign on his own, declaring himself king. Theon remains with his father and starts raiding the Stony Shores.
Catelyn Stark travels South to Renly Baratheon, Robert’s younger brother, who also declared himself king and managed to gather an impressive army through his marriage with Margaery, Mance Tyrel’s daughter. Catelyn hopes that she will be able to convince Renly to side with Robb and fight against the Lannisters but Renly refuses. He decides however to go against his older brother, Stannis Baratheon, who also declared himself king and make Catelyn watch how he destroys his brother’s army.
The night before the battle was to take place, Renly is killed in a suspicious manner by a shadow that entered his tent while Catelyn and one of Renly’s guards were there. Catelyn runs away with warrior-maid Brienne of Tarth, fearing that they will be blamed for Renly’s death.
As a result, many lords that supported Renly joined Stannis’ side. Stannis advances with his new army towards Storm’s End where is meet with resistance from the castellan who refuses to surrender until he sees Renly’s body.
The lords that sided with Stannis try to convince him to attack Storm’s End, sure on their power. Stannis refuses and convinces Ser Davos, one of his most loyal men, to smuggle Melisandre, a red priestess of the eastern god R'hllor, into the castle. Ser Davos does so only to see her give birth to a black shadow with Stannis’ face. That night, the castellan dies in suspicious circumstances and Storm’s End falls without further battles.
At Winterfell, Bran remains to rule in his brother’s place. He receives the lords that have come to swear their allegiances while also being plagued by strange dreams. The arrival of Jojen and Meera Reed sheds some light on the nature of his dreams. Jojen tells Bran that the dreams he has are not common ones, but rather prophetic dreams.
Bran is forced to surrender the castle after Theon Greyjoy captures Winterfell with a small group of Iron men. His sister advices him to give up Winterfell as Theon didn’t have enough man power to hold it long enough but he ignores his sister’s advice and remains at Winterfell.
Fearing that he doesn’t have enough power in case the northmen decide to take back Winterfell, Theon sends Reak, Ramsay Snow’s servant, to gather men to protect Winterfell. During the time Reak is gone, Bran, Rickon, Hodor, Jojen, Meera and Osha manage to run away. Theon goes looking after them and returns after a while with two dead boys that Theon presents as being Bran and Rickon.
A large group of northmen appears and starts attacking Winterfell. The northmen are however defeated by an army lead by Reak who was actually Ramsay Snow. Theon opens the gates for them but is taken captive and Winterfell is burned. Shortly after, Bran and the others emerge from the crypt where they hid during the battle. They decide to split up, Osha taking Rickon with her and the others going north.
In King’s Landing, Tyrion is appointed as the Hand of the King despite his sister’s protests. Tyrion slowly starts to remove his sister’s men from key positions and replace them with men loyal to him. Tyrion makes efforts to ensure that King’s Landing will be safe if Stannis decides to attack it. He secures and allegiance with Prince Doran Martell who agrees to marry his son Trystane to Joffrey's sister Myrcella and he also sends Tommen away in case Joffrey happened to be killed in the inevitable battle. Tyrion also sends Petyr to Highgarden, hoping to get house Tyrell on their side.
During this time, Robb Stark leads his northern army into the westerlands and emerges victorious from a number of battles against Lannister forces, winning a battle at Oxcross and storming Ashemark and the Crag. Because of this, Sansa has to suffer from Joffrey’s wrath when he finds out about Robb’s victories.
Tywin reluctantly emerges from Harrenhal and attempts to pass the fords near Riverrun, where he is stopped by Edmure Tully, Catelyn's brother and the infirm Lord Hoster's heir. Although this prevents the Lannisters from falling on Robb's rear, it allows them to rapidly march south to join their new allies, the Tyrells.
After Tywin lefts Harrenhal, the castle is taken by Roose Bolton.
Arya Stark is one of the people that serve at Harrenhal. In the beginning of the book, she is taken by Yoren to the Wall. On the road, they meet with soldiers sent after one of the boys in Yoren’s group, a blacksmith apprentice named Gendry. Yoren refuses but they are eventually attacked by Lannister freeriders who kill almost the entire group. Arya manages to help a group of criminals bound in a cage before she escapes the battle with Gendry, Hot Pie and Lommy.
They are eventually recaptured by soldiers led by Gregor Clegane. Lommy is killed because of a leg injury but the others are taken to Harrenhal and made servants. During her time at Harrenhal, Arya meets with one of the captives she helped, Jaqen H'ghar, who lets her choose three people she wants for him to kill as a way of repaying the fact that she saved him and two others.
For her three choices, Arya selects Chiswyck, a soldier in Gregor Clegane's forces, Weese, her servant overseer, and Jaqen H'ghar himself. The first two murders he carries out without question; in lieu of the third choice, Arya leverages H'ghar to help her slay the Lannister soldiers guarding Robett Glover, who had been taken prisoner by the Brave Companions. After Glover is freed, the Brave Companions turn their cloaks and join with the North. Control of Harrenhal is ceded to Roose Bolton, whom Arya serves as cupbearer.
Arya escapes shortly after Roose Bolton takes Harrenhal. She kills one of the guards and, together with Gendry and Hot Pie, runs away.
Meanwhile, King’s Landing is attacked by Stannis. The majority of Stannis’ fleet is destroyed with wildfire but Stannis’ men still advance towards the city. Tyrion led a group of soldiers that push Stannis’ forces away from the north shore, but Tyrion is heavily wounded when Ser Mandon Moore, a member from the Kingsguard, tries to kill him.
The Battle of Blackwater ends when Stannis’ fleet is destroyed by Tywin and the Tyrells.
The book ends with the Tyrells asking that Joffrey breaks his engagement with Sansa and marries Margaery. Despite having her engagement broke off, Sansa remains in King’s Landing.