Thompson began the most controversial part of his Confederate career in the spring of 1864. He and Clement Claiborne Clay, a former U.S. Senator from Alabama, were sent by Davis as special Confederate agents to Canada. The purpose of the mission, as explained by Confederate secretary of state Judah P. Benjamin, was to provoke a "disruption between the Eastern and Western States in the approaching election at the North." Supplied with a war chest of $300,000, Thompson was to do all in his power to demoralize the Union home front.

Clement Alexander Finley was born on May 11, 1797 in Newville, Pennsylvania.  His family moved very soon after to Chillicothe, Ohio when his father, a cavalry hero of the Revolutionary War, received a sizable plot of land for his war service.  Young Clement was educated in local schools and then returned to Cumberland County to enroll at Dickinson College with the Class of 1815.  A tall and reputedly handsome young man, he graduated with his class and then studied medicine at the University of Pennsylvania, receiving his M.D.

The kidnapping plot evaporated when the city of Richmond fell and the war ended. Five days later, on 14 April 1865, Booth learned that President Lincoln planned to attend Our American Cousin (starring Laura Keene) at Ford's Theatre. Working quickly, Booth assigned [George] Atzerodt to assassinate Vice President Andrew Johnson and [Lewis] Payne to kill Secretary of State William Seward while Booth himself murdered Lincoln.

An early incident revealed Boyd's commitment and courage and ironically brought her praise from Federal officers. After Boyd's father left to join Thomas J. "Stonewall" Jackson's infantry, Union troops invaded Martinsburg on 3 July 1861. The next day, Union soldiers forcibly entered the Boyd home and prepared to hoist the Federal flag and remove the Confederate flags in Belle's room and outside the house. Mary Boyd's protests provoked an officer to address her "in language as offensive as it is possible to conceive," as Belle recalled in her 1865 memoir Belle Boyd in Camp and Prison.