Botts aligned with the United States Constitutional Union Party and supported John Bell. Though Bell was outpolled nationally by both the winning candidate Republican Abraham Lincoln and the Northern Democrat Stephen A. Douglas, Botts continued to support the principles of the Constitutional Union party. Even Carroll before her death acknowledged Botts was too outspoken and brusque to attract enough support. Botts failed to attract sufficient support as a Unionist delegate to attend Virginia's Secession Convention of 1861, although fellow Unionist John Brown Baldwin was elected. President Lincoln met separately with Baldwin and Botts, who later published different accounts of their meetings, neither of which stopped Virginia from seceding. Botts blamed Baldwin for keeping Lincoln's peace offer secret while his native state moved toward secession. He retired to his Henrico County farm after Virginia declared its secession in the American Civil War, but continued to write letters to newspaper editors and remained uncompromisingly Unionist in his sentiments. Through the war, Botts refused to fight against Virginia, but remained in the Commonwealth. On March 2, 1862, Richmond's Confederate provost marshal John H. Winder jailed Botts and fellow Unionist Franklin Stearns without trial for espousing Unionist positions after the Confederacy suspended the right of habeas corpus. About 150 people were eventually picked up, and Stearns was later placed under house arrest in his Richmond warehouse, where his family could care for him. Botts stated that while he was in captivity Captain George W. Alexander attempted to persuade him to join the Confederate army as a brigadier general in exchange for his freedom. Botts spent eight weeks in solitary confinement. He was released after promising not to publish any more incendiary letters, and in January 1863 moved to a plantation he had won gambling, Auburn, in Culpeper County, Virginia, where Botts entertained both Union and Confederate officers at various times. Botts had promised he would move away from Richmond to ensure his pardon. He was arrested on October 12, 1863, by order of Confederate General J. E. B. Stuart, for entertaining Union officers (although three of his slaves had absconded for Union lines and he requested their return but was denied), but released later the same day. Postwar In 1864, the rump general assembly at Alexandria attempted to elect Botts to the U.S. Senate, but he declined. On the night of President Lincoln's assassination, several men arrived at his house and attempted to rob