During the War of the Five Kings, Roose fought for his liege, Robb Stark. Chosen to lead the Stark armies at the Battle of the Green Fork, Bolton suffered a decisive defeat, and was forced to retreat north, while a large part of his forces were held prisonner at Harrenhal. When Tywin Lannister vacated the castle, however, Arya Stark secretly liberated the men held captive, who proceeded to take over the castle. Arya went on to be his cupbearer under the name Nan for a brief time. When Robb Stark declared himself King in the North, Roose pledged aliegence to him.
Secretly, Roose had plotted with Tywin Lannister against his liege, and, following the Red Wedding (In which the King of the North, his mother, and most of his retinue were murdered), Roose became Warden of the North, and the de jure lord of Winterfell, due to his bastard son's marriage to Jeyne Poole, who was disguised as Arya Stark.