After the Union Army regained control of Nashville in early 1862, Etheridge returned to the city and spoke before a crowd of 1,200. He threw his support behind Andrew Johnson, who had by then been appointed Military Governor of Tennessee. Etheridge turned against the Lincoln Administration after Lincoln issued the Emancipation Proclamation, as he considered its issuance a betrayal of his promise to Southern Unionists not to tamper with slavery. In December 1863, he joined an unsuccessful plot to give Democrats and Southern Unionists control of the House, using his position as Clerk to try and invalidate the credentials of Republican congressmen. In response, the House voted to replace him as Clerk that same month.