Across the narrow sea from Westeros, Daenerys Targaryen, the last descendant of the king that Robert Baratheon deposed, leads the remnants of her khalasar (nomadic tribe) through a wasteland. She carries the three dragons that hatched in her husband’s funeral pyre, a fire she entered and emerged from unharmed. Many of her people have fled or died, and those who remain are near collapse when they come across an abandoned city. Even Ser Jorah Mormont, an exile from Westeros who serves as her advisor and confidante, does not recognize the city, but they decide to camp there. Daenerys sends out three scouts to see if any other civilizations can be found nearby. Two of the scouts find nothing. Eventually the third scout returns in the company of three people from the great city of Qarth, who have come to see Daenerys and her dragons.
North of the Wall, Jon and the party from the Night’s Watch pass several abandoned wildling villages. The people seem to have vanished, though there are no signs of attack. The Old Bear decides to continue pressing northward, where they will meet up with another party of men from the Night’s Watch to see if they can figure out what has happened.
Yoren leads the party to a vast lake known as the God’s Eye, where they hope to find boats to sail to Harrenhal. They reach an abandoned town, but it has no boats. The group camps in the town's holdfast, basically a small fort, for the night. They are awakened by the arrival of a Lannister raiding party under the command of Ser Armory Lorch. Yoren refuses to let the party enter the holdfast, so Lorch’s men attack. Arya and the others fight back, killing several, but the Lannister forces breach the walls and begin burning the holdfast. Yoren tells Arya to take as many boys as she can through a trap door in the barn, where they can hide. Arya brings the crying girl they found earlier in the abandoned village, and Lommy, Hot Pie, and Gendry also make it into the hiding place. Before diving through the trap door, Arya frees Jaqen H’ghar and the other two prisoners.
Cersei furiously demands that Stannis’s letters about Joffrey’s incestuous parentage be burned, but Tyrion points out that everyone has heard the story by now and that Stannis’s apparent religious conversion can be used against him. Littlefinger proposes that they spread a rumor that the real father of Stannis’s daughter is Patches, the fool. Tyrion and his squire, Podrick Payne, meet with the city’s blacksmiths. Tyrion asks them to build a vast iron chain but doesn't tell them why. Tyrion goes to a brothel run by a woman named Chataya. There, a prostitute named Alayaya leads him into a closet, where he descends a ladder to a secret tunnel where Varys awaits. They travel through the tunnel and emerge in a stable so that Tyrion can take a horse to the house where he is hiding Shae. He asks whether Varys told Stannis about Joffrey’s parentage. Varys denies it and hints that Littlefinger may have spread the story.
At Winterfell, Bran hosts many northern lords and ladies loyal to the Starks. Bran has Hodor, a huge mentally disabled stableboy, carry him down to the courtyard to watch young men who are practicing fighting. The Frey boys mock Hodor, angering Bran, but Maester Luwin intervenes. Luwin chastises Bran for neglecting his duties with their adult guests.
Bran joins Luwin and Ser Rodrik Cassel, Winterfell’s master of arms, in the great hall to hear requests from the lords and ladies. Lady Donella Hornwood, whose husband and son died fighting the Lannisters, tells them that Ramsay Bolton, the bastard son of Lord Roose Bolton, and his sinister companion Reek are massing men at the Dreadfort near Hornwood lands. Rodrik advises her to marry again, and Luwin points out what a dangerous situation she is in. Bran proposes letting Ramsay Bolton become the heir, but to no effect. Bran has Hodor take him to the godswood, where they find Osha, a wildling servant of Winterfell, swimming. Osha asks Bran about his wolf dreams, but he lies and says that he has not had any others.
The next day, several more lords visit and propose themselves as suitors to Lady Hornwood. Rodrik, Luwin, and Bran discuss what should be done. They do not see an easy solution, though Luwin wonders if Bran’s idea about letting Ramsay Bolton become the heir might be best. Another visitor brings word of Stannis’s letter and the incestuous affair between Cersei and Jaime Lannister. This news shocks Bran into remembering that he did not fall from Winterfell’s walls, but was pushed by Jaime.
This section of A Clash of Kings moves between all three of the novel’s main plot lines—the civil war in Westeros, the mysterious events north of the Wall, and, for the first time, the action across the narrow sea, where Daenerys Targaryen has brought dragons back into the world. These three stories may initially appear to be only distantly related to one another, but they share strong thematic connections. Specifically, each involves one or more characters coming of age and learning to be a leader. In Westeros, Bran Stark finds himself in charge of Winterfell though he is not even a teenager yet, while his older brother Robb finds himself at the head of an army and bearing the title King of the North. Jon Snow, meanwhile, is becoming a leader in his own right among his peers in the Night's Watch. Finally, the young Daenerys Targaryen is suddenly leading a khalasar through a foreign land.
As is the case with both Robb and Bran, Daenerys finds herself in a leadership role at an incredibly young age. Just a teenager, she has responsibility for the remains of her khalasar. But her situation also differs from theirs in significant ways. Whereas Robb and Bran have authority because of their family name, Daenerys’s khalasar follows her out of a mix of personal loyalty and awe: not only could Daenerys not be killed or maimed by fire, but she has also brought three dragons into the world. As not a single dragon has been seen for centuries, Daenerys has an almost supernatural aura about her, and the end of her chapter makes clear that her dragons are going to be at the center of her development.
Notably, Daenerys, Jon, and Arya all move through desolate landscapes, where homes, villages, towns, and even an entire city have been abandoned. The novel presents each of these abandoned landscapes in a slightly different way: the area around God’s Eye has been abandoned because of war, while the land Daenerys crosses is empty because it is environmentally inhospitable and the villages north of the Wall have emptied for reasons that remain mysterious. Despite these differences, each character encounters the same thing, the absence of civilization. Whether from war, natural causes, or forces unknown, civilization has vanished from these places. In these chapters, the novel shows how tenuous social life is and how easily it can be destroyed. It also sets an ominous tone that suggests the characters will face greater dangers ahead.
Arya’s chapter reveals the complete breakdown of the old social order in Westeros, but it also shows Arya's own resourcefulness and strong sense of morality. Where once the men of the Night’s Watch were respected by everyone and treated with generosity, now they must move furtively across the war-torn landscape, trying to avoid notice by the rampaging war parties. The lack of social order is evident in Ser Amory Lorch's decision to attack the party even knowing Yoren is with the Night's Watch. It suggests law and order have deteriorated so much that Lorch knows there will be no consequences to his actions. There is no force to arrest him or court to punish him. That he attacks a party of mostly children and teens only serves to emphasize the lack of moral order in Westeros. Arya holds her own against the soldiers as she depends on what little training she's received. More notably, however, despite the dangers of her situation she retains enough conscience to save the orphaned girl and release the prisoners, who would have otherwise burned to death. The contrast between Arya's actions and those of the Lannister men makes her seem all the more noble and moral.
We also see the division between Tyrion and Cersei deepening in this section, and the conflict emphasizes the difference in their natures. Cersei wants to take a hard line against Stannis’s letter revealing her and Jaime's incest, burning the copies and punishing anyone who talks of it. Tyrion disagrees with her, setting up another conflict between the two. He thinks that Cersei’s plan will only convince people that Stannis tells the truth. Their respective approaches to the situation reveal a great deal about their characters. Cersei acts out of pride and passion, but Tyrion acts pragmatically. He recognizes the truth of Stannis’s accusation. Rather than try to hide it, he seeks to control the damage it can cause. This difference in approaches suggests that the struggle between Tyrion and Cersei will not be a short or simple one, as they approach the world from very different points of view.
Where earlier the novel showed readers the mystical side of Bran’s story, now it shifts focus, emphasizing the political difficulties in Winterfell and Bran's need to grow up. Bran wants to be a boy playing with the other boys, and his altercation with the Freys demonstrates how much he remains a child. But he must also sit through the political discussions with the lords and ladies loyal to Winterfell, and his suggestion about Ramsay Bolton appears to be a smart one, as it is taken seriously by Luwin. These events indicate that, though he may not want to, Bran must grow up, but also that he is capable of growing into a capable and intelligent leader.