 He lost his seat due to Virginia's secession from the Union.During the Civil War, Whaley recruited men for the Union Army.Commissioned as major of the 9th West Virginia Volunteer Infantry Regiment, Whaley was captured by Confederate forces under the command of General Albert Gallatin Jenkins on November 10, 1861, during a Confederate raid on the town of Guyandotte, West Virginia (now a neighborhood of Huntington, West Virginia).