Blackburn remained in Canada to avoid prosecution by U.S. authorities, but he returned to his home country in 1868 to help combat a yellow fever outbreak along the Gulf Coast of Texas and Louisiana.

He rehabilitated his public image by rendering aid in yellow fever outbreaks in Memphis, Tennessee, in 1873, Fernandina, Florida, in 1877, and Hickman, Kentucky, in 1878.

Troubled by the conditions at the penitentiary in Frankfort, Blackburn attempted to ease overcrowding through liberal use of his gubernatorial pardon, earning him the derisive nickname "Lenient Luke".

[8] Just before Cary's birth, Blackburn invested heavily in the hemp rope and bagging industry and suffered a significant financial loss when the business venture subsequently failed.

[8] Luke Blackburn quickly became an active member of the community, helping found a temperance society, joining a militia group, and becoming the administrator of a local hospital.

[11] In 1848, Blackburn served as the city's health officer and implemented the first successful quarantine against a yellow fever outbreak in the Mississippi River valley.

[13] A brief poem written by Blackburn indicates that the couple had a daughter named Abby, but the child apparently died as an infant, and her birth and death dates are unknown.

[16] After securing sufficient medical supplies for the wounded, Blackburn traveled to Richmond, Virginia, to meet with Confederate Secretary of War James Seddon and offered to serve as General Inspector of Hospitals and Camps without taking compensation or a rank.

[5] Blackburn and his wife left Mississippi for Halifax, Nova Scotia, in August 1863, then continued on to Toronto (in what was then the Province of Canada) where they lodged in a boardinghouse.

[22] Although little is known of his actions in Canada for the remainder of the war, he was rumored to have been part of a plot to incite massive insurrections in New England as a diversion, allowing fellow Confederate agent Thomas Hines to lead a prison break at Camp Douglas in Chicago.

[23] When word of the plot was leaked to Union officials, they sent troops to reinforce Boston, Massachusetts, Blackburn's rumored target, quashing his role in the operation.

[23] On April 12, 1865, just days after the last major battle of the Civil War, a Confederate double agent named Godfrey Joseph Hyams approached the U.S. consul in Toronto claiming to have information about a plot by Blackburn to infect Northern cities with yellow fever.

[24] According to Hyams, he had agreed to help Blackburn smuggle trunks of clothes used by patients infected with yellow fever into Boston, Massachusetts; Philadelphia, Pennsylvania; Washington D.C.; New Bern, North Carolina; and Norfolk, Virginia (the latter two cities being occupied by Union troops).

[19][20][22] Hyams said he was instructed to sell the trunks' contents to used clothing merchants,[22] and that Blackburn, subscribing to the common nineteenth century belief that yellow fever could be spread by contact, hoped that by dispersing the "contaminated" articles throughout these major cities he could trigger an epidemic that would cripple the Northern war effort.

[22] Hyams further alleged that Blackburn had filled a valise with fine shirts and instructed him to deliver it to President Abraham Lincoln at the White House, saying they were from an anonymous admirer.

[20] According to this information, Blackburn contracted with Edward Swan, a hotel owner in St. George's, to store them until mid-1865 and then ship them to New York City, in an attempt to start an outbreak there.

[25] Acting on this intelligence, Bermudan officials raided Swan's hotel and found three trunks of garments and linens with stains consistent with the "black vomit" symptomatic of yellow fever.

[26] Writing in the journal America's Civil War, U.S. Navy physician J. D. Haines notes that the Confederate agents who testified against Blackburn were of dubious reputation.

[20] Haines also points out that Blackburn's previous reputation as a humanitarian was ignored; in the hysteria following Lincoln's assassination, conspiracy theories abounded and Northerners were inclined to believe the worst about anyone with Confederate sympathies.

[22] When he learned of a yellow fever outbreak in New Orleans and the Texas Gulf Coast, Blackburn wrote to President Andrew Johnson on September 4, 1867, asking permission to return to the U.S. and help treat the disease.

Some towns in the Jackson Purchase region attempted to implement crude quarantines, but the city of Louisville completely ignored Blackburn's advice and welcomed refugees from the South.

[39] On September 5, the mayor of Hickman, Kentucky, a small western town along the Mississippi River, telegraphed the state board of health, informing them that yellow fever had reached epidemic levels in the city and requesting that Blackburn be sent to them as soon as possible.

[45] He sought relief from his ailments at Crab Orchard Springs, while much of the campaign oratory was delivered on his behalf by fellow Democrats Boyd Winchester, Parker Watkins Hardin, W. C. P. Breckinridge, and others.

In the wake of the Gazette's investigation, other Northern newspapers, including the Canton Repository, Cleveland Herald, and Philadelphia Press, derided Kentuckians for even considering the election of Blackburn (who they nicknamed "Dr. Blackvomit").

Blackburn did not respond to the accusations, and Kentucky Republicans barely made mention of it, knowing that the northern press in general and the Cincinnati Gazette in particular were widely distrusted in the state.

Kentucky newspaper editor Henry Watterson opined that most Kentuckians already knew about Blackburn's Civil War activities and either explicitly approved of them or were apathetic about events that had occurred a decade and a half earlier.

[56] The poor conditions at the penitentiary were partially because the state leased management of the facility to private contractors, who frequently neglected prisoners' needs to cut costs.

[57] These contractors often provided benefits such as cheap laundry services and free meals to legislators to secure contracts and encourage them to ignore their abuse of prisoners.

[64] They decried his record number of pardons and resented the fact that he did not give more consideration to party service and loyalty when appointing individuals to state jobs.

[64] Having announced at the beginning of his term that he would seek no further political office, Blackburn nonetheless attempted to defend his record in a speech at the 1883 Democratic nominating convention, but boos and shouts for him to sit down almost drowned out the address.