Season two spans several months on a world where the seasons last for years at a time. The Seven Kingdoms are at war, with the King in the North, Robb Stark, fighting to win independence for his people and those of the Riverlands. Robb decides that he must win the allegiance of the fiercely independent ironborn to his cause, and sends his best friend Theon Greyjoy to treat with his father, who is hatching plans of his own. Meanwhile, Joffrey Baratheon holds the Iron Throne with the backing of the powerful House Lannister, but his uncle Renly has also claimed the throne with the support of House Tyrell, whose armies are much larger. As they struggle for the throne, Tyrion Lannister arrives in King's Landing to take matters in hand, only to face opposition from his scheming sister, Cersei, now the Queen Regent.

However, there is another faction entering the picture. Stannis Baratheon, Robert's younger brother and Renly's older, has also claimed the Iron Throne. A proven battle commander and veteran of several wars, Stannis is known to be utterly without mercy to his enemies and will do what is right even if it destroys him. Advising him is Melisandre, an enigmatic priestess from the east, who believes Stannis is meant for a greater destiny, and Ser Davos Seaworth, an honest and honorable man uneasy with the shifts in power at Stannis' court.

Far to the east, Daenerys Targaryen has hatched the only three dragons in the world. Eventually they will grow into terrifying monsters capable of destroying cities at her command, but for now they are still hatchlings and vulnerable. With her khalasar gone, Daenerys and her small band of followers must find a way across a forbidding wasteland and find new allies to support her claim to the Iron Throne.

In the distant north, the Night's Watch has mounted an expedition beyond the Wall, searching for missing rangers and investigating rumours of wildlings gathering in the mountains. For Jon Snow this will be a rite of passage as he is asked to make difficult choices, for the realm and for himself.