 While being marched up the Guyandotte River, Major Whaley escaped his captors at Chapmanville in Logan County and made his way to safety by traveling up Big Harts Creek in Lincoln and Logan counties to Queens Ridge in Wayne County, West Virginia.After creation of the new state of West Virginia, Whaley won election from West Virginia's 3rd congressional district as an Unconditional Unionist, serving from 1863 to 1867.From 1863 to 1865, he was chairman of the Committee on Invalid Pensions.