In 1811, already suffering from ill health, Scott applied for a pension so that he could retire, but was refused. During the War of 1812, the administration sought to ensure the loyalty of its subjects by imposing martial law and, in 1814, by prosecuting those who had expressed sympathy for the enemy with treason in a series of trials at Ancaster known as the "Bloody Assize". Fifteen men were condemned to death of which eight were executed. These actions increased Scott's workload.
In 1816, Scott was finally granted a pension and retired. He was succeeded by William Dummer Powell as Chief Justice for the province. Scott died at York (Toronto) in 1824.