He married Hannah Turner and began the construction of a large manor house on land given him by his father, Zedekiah Stone.

Re-elected in a bid for a second term in the House, Stone resigned when he was elected to the United States Senate by the North Carolina General Assembly in late 1800.

He resigned his seat in the Senate in 1807 to return to the state Superior Court, but was there for only a year before being elected Governor of North Carolina by the legislature in November 1808.

As Governor, Stone was an ardent supporter of agricultural and industrial development, as well as of the expansion to the education system to both sexes and all social classes.

Stone's second term in the U.S. Senate lasted only a year; he was censured by the NC General Assembly for failing to support the administration during the War of 1812.