[1] During the American Civil War, he sympathized with the Confederacy, but returned to what had become West Virginia for his final years.

[13] Johnson initially became active in local politics as a member of the Democratic-Republican Party (aligned with President Thomas Jefferson).

In 1814, Captain Johnson and Captain John McWhorter of the other company led their riflemen to Norfolk, where Johnson and his men helped keep the peace until the war's end in 1815, while McWhorter's men headed west under General (and future President) William H. Harrison to fight in Ohio.

[18] In 1847, Johnson again ran for election to the Virginia House of Delegates and was reelected the following year, again serving part-time while pursuing his farming and other business interests.

During the Virginia Constitutional Convention of 1850 and 1851, Johnson was one of the four delegates from the west-of-the-Appalachians district consisting of Wood, Ritchie, Harrison, Doddridge, Tyler, and Wetzel Counties, alongside John F. Snodgrass, Gideon D. Camden and Peter G. Van Winkle.

[20] The only Virginia governor from west of the Allegheny Mountains began his gubernatorial duties under the new constitution on January 1, 1852.

[21] As governor (and prohibited by the constitution from succeeding himself), Johnson granted clemency (sale out of state) to three enslaved people convicted for murders in and near Richmond in highly publicized cases.

Phillis had been convicted of murdering a crying child under her care by administering morphine; Jordan Hatcher had killed a white overseer in a Richmond tobacco factory who was whipping him; young Lucy had attempted to conceal a pregnancy and ingested laudanum and camphor while giving birth in an outbuilding and the infant's corpse was later found.

[24][25] When U.S. Army soldiers occupied Bridgeport, Johnson moved his household eastward across the Appalachians to Staunton, where he remained for the rest of the war, during which the State of West Virginia was created, in part through Carlile's and Pierpont's efforts.

His nephew, Waldo P. Johnson, who had become a lawyer in Harrison County before moving to Missouri in 1842 (where he served in that state's legislature and then became a U.S.

In 1866, Johnson, who had returned to Bridgeport after the conflict, formally joined the Simpson Creek Baptist Church, in whose churchyard his wife had been buried 13 years before.

He died at his home, Oakdale, in Bridgeport in 1877 and was buried beside his wife and young children in the old Brick Church Cemetery.