A Clash of Kings is the story of a war between several claimants to the Iron Throne of Westeros, a fantasy world once ruled by dragons and sorcerers but now fallen to squabbling among noble houses. The Starks and Lannisters, two of the kingdom's dominant families, wage a destructive war that lays waste to Westeros while across the ocean the true heir to the throne, Daenerys Targaryen, struggles to keep her fledgling court, and dragons, alive.
A Clash of Kings depicts the Seven Kingdoms of Westeros in civil war, while the Night's Watch mounts a reconnaissance to investigate the mysterious people known as wildlings. Meanwhile, Daenerys Targaryen continues her plan to reconquer the Seven Kingdoms.
With King Robert Baratheon dead, his son Joffrey Baratheon and brothers Renly and Stannis all claim the throne of Westeros. Robb Stark is declared 'King in the North' while Balon Greyjoy declares himself king of the Iron Islands and attacks the western coast of the North. Robb's younger brother Bran Stark finds new friends in Jojen and Meera Reed.
Stannis Baratheon declares himself King of Westeros, encouraged by Melisandre of Asshai, a priestess who believes Stannis the reincarnation of Azor Ahai, a messianic figure of her faith. The war is dubbed the War of the Five Kings. Catelyn Stark, under orders from her son King Robb Stark, meets Renly and Stannis to discuss alliance against the Lannisters; but the meeting fails, and a shadow-creature created by Melisandre kills Renly. Brienne of Tarth and Catelyn Stark are incriminated in Renly's murder and most of Renly's supporters defect to Stannis, except the Tyrells. Renly's stronghold, Storm's End falls when Melisandre's second shadow kills its castellan, Cortnay Penrose.
Tyrion Lannister arrives at King's Landing as acting Hand of the King, the closest adviser to the monarch Joffrey. Whilst intriguing against Joffrey's mother, the Queen Regent Cersei, Tyrion improves the defenses of the city and sends Littlefinger to negotiate with the Tyrells, betrothing Joffrey to Margaery Tyrell, despite his earlier betrothal to Sansa Stark. Tyrion also forges an alliance with House Martell when he betroths Joffrey's sister Myrcella to Trystane Martell.
To conquer the North and to impress his father Balon, Theon Greyjoy captures Winterfell, taking Bran and Rickon captive; but Bran and Rickon disappear in the night. Rather than admit his failure, Theon murders two anonymous peasant boys similar in size to Bran and Rickon and mutilates their faces to enhance the resemblance. Believing this ruse, Stark supporters besiege the castle, joined by a force from House Bolton. Theon having conspired with Bolton's bastard son, Ramsay Snow, the Bolton soldiers turn on the besiegers and Theon opens the gates to the victorious Boltons, whereupon they destroy Winterfell, slaughter its inhabitants and take Theon prisoner. Osha, a captured wildling turned castle servant, takes Rickon to safety while Bran, accompanied by Meera, Jojen, and his simpleton manservant Hodor, travels north. Robb Stark wins several victories against the Lannisters, and Tywin Lannister advances against him, but receiving news that King's Landing is threatened, withdraws.
Arya Stark, posing as a boy named 'Arry', travels with new recruits for the Night's Watch. They are captured and taken to Harrenhal, where Arya poses as a serving girl. When a man named Jaqen H'ghar offers to repay Arya for saving himself and his two companions by killing three men of her choice, Arya selects two Lannister bannermen and threatens Jaqen himself unless he releases the Stark supporters, who overtake the castle. His debt repaid, Jaqen gives Arya an iron coin and a strange phrase, "Valar Morghulis", to be used in asking help from his compatriots. When Lord Roose Bolton occupies Harrenhal, Arya becomes his cup-bearer, but soon escapes.
In the Battle of Blackwater Bay, Stannis Baratheon's army reaches King's Landing and launches assaults by both land and sea. The Baratheon forces vastly outnumber the Lannister defenders but under Tyrion's command, the Lannister forces use "wildfire" (similar to Greek fire) to ignite the bay, and raise a massive chain across its mouth to prevent Stannis's fleet from retreating. Stannis's attack fails when Tywin Lannister leads his army (and the remaining forces under Mace Tyrell) to King's Landing. During the battle, Ser Davos Seaworth is nearly killed when his ship is destroyed by wildfire. Stannis's fate is left uncertain. During the defense of the castle, Tyrion is attacked by one of Joffrey's guards, and rescued by his squire, Podrick Payne.
A scouting party from the Night's Watch learn that the wildlings are uniting under 'King-beyond-the-Wall' Mance Rayder. The Watch then continue to an ancient hill-top fortress known as the Fist of the First Men, whence Jeor Mormont sends Jon Snow and Qhorin Halfhand with others to the Skirling Pass, where they are hunted by wildling warriors. Facing certain defeat, Halfhand commands Snow to infiltrate the wildlings and learn their plans. They are captured by wildlings who demand Jon fight Qhorin to join them. Jon kills Qhorin with the aid of his direwolf, Ghost and Jon learns that Mance Rayder is advancing on the Wall with thirty-thousand wildlings, giants, and mammoths.
Daenerys Targaryen travels east, accompanied by the knight Jorah Mormont, her remaining followers, and three newly hatched dragons. Scouts find a safe route to the city of Qarth, where her dragons make Daenerys notorious. Xaro Xhoan Daxos, the leader of the Thirteen, a prominent group of traders in Qarth, initially befriends the outsiders; but Daenerys cannot secure aid in claiming the throne of Westeros, because she refuses to give away any of her dragons. As a last resort, Daenerys seeks counsel from the warlocks of Qarth, who show Daenerys many confusing visions and threaten her life, whereupon one of Daenerys's dragons, Drogon, burns down the warlocks' "House of the Undying". An attempt to assassinate Daenerys is thwarted by a fat warrior named Strong Belwas and his squire Arstan Whitebeard: agents of Daenerys's ally Illyrio Mopatis, who have come to escort her back to Pentos.