The Baltimore Plot concerned alleged conspiracies in February 1861 to assassinate President-elect of the United States Abraham Lincoln during a whistle-stop tour en route to his inauguration. Allan Pinkerton, founder of the Pinkerton National Detective Agency, played a key role in managing Lincoln's security throughout the journey. Though scholars debate whether or not the threat was real, Lincoln and his advisors clearly believed that there was a threat and took actions to ensure his safe passage through Baltimore. He ultimately arrived secretly in Washington, D.C., on February 23, 1861.

A planned train route through Bellaire, Ohio, to Wheeling, Virginia (West Virginia had yet to break off from Virginia) and eastward was subsequently rerouted up through the Pittsburgh vicinity, through Pennsylvania, into Maryland, and eventually to Washington. He passed through Baltimore unnoticed, which proved controversial after newspapers revealed the seemingly cowardly decision. The incident and its significance have since been debated by scholars.

On November 6, 1860, Lincoln was elected as the 16th President of the United States, a Republican, and the first to be elected from that party. Shortly after his election, many representatives from the South made it clear that the Confederacy's secession from the U.S. was inevitable, which greatly increased tension across the nation.

Allan Pinkerton was commissioned by the railroad's president, Samuel M. Felton, to provide security for the president-elect on his journey to Washington, D.C. The only north-south rail line to Washington was through Baltimore, making it necessary for Lincoln to cross Maryland to reach the capital, therefore potentially dangerous for the Republican president-elect to pass through a city in which he received only two percent of the vote, and through a state in which he received "fewer than 2,300 votes".

The incoming Republican government was not about to take risks, and later that year Lincoln would suspend many civil liberties, even ordering the arrest of Maryland's state legislature for fear it might vote for secession. Pinkerton, in particular, was extremely cautious, which he would demonstrate during the coming war, when he repeatedly overestimated Confederate strength and negatively influenced Union Army policy.

On February 11, 1861, President-elect Lincoln boarded an eastbound train in Springfield, Illinois, at the start of a whistle-stop tour of 70 towns and cities, ending with his inauguration in Washington, D.C. Allan Pinkerton, head of the Pinkerton Detective Agency, had been hired by railroad officials to investigate suspicious activities and acts of destruction of railroad property along Lincoln's route through Baltimore. Pinkerton became convinced that a plot existed to ambush Lincoln's carriage between the Calvert Street Station of the Northern Central Railway and the Camden Station of the Baltimore and Ohio Railroad. Pinkerton and his fellow operatives, including Kate Warne, discovered several possible plots in Baltimore. This included an investigation of Corsican hairdresser Cipriano Ferrandini, a well-established barber at Baltimore's Barnum's Hotel, and president of the pro-Confederate National Volunteers. One of Pinkerton's operatives attended a meeting in which Ferrandini made a fiery speech condemning Lincoln; after interviewing Ferrandini, they learned of several reported plans to assassinate Lincoln. While only reports from Pinkerton's operatives tied Ferrandini to the assassination conspiracy, he traveled to Mexico in 1860 to "train with a secessionist militia" and met Jerome N. Bonaparte and Thomas Winans, two individuals in the high society of Baltimore who had Confederate sympathies.

Later, Pinkerton's operatives investigated Otis K. Hillard, a member of the Palmetto Guards, a secret military organization in Baltimore. After interviewing him, they learned of several possible plots to kill Lincoln, including one where Lincoln would be surrounded by a "vast crowd" at the Camden Street depot. Another Pinkerton operative, Timothy Webster, learned about a secret league from Baltimore which had planned on destroying railroad bridges and telegraph wires and killing Lincoln. Other individuals, such as Senator William Seward and New York City police detective David S. Bookstaver, drew conclusions similar to Pinkerton's, while a congressional select committee also investigated the threat by Ferrandini. However, the committee determined that the threat wasn't real and that the evidence was not substantial. Pinkerton agents also investigated another secret society, the Knights of the Golden Circle, a White supremacist organization, which planned to create "a new nation dominated by slavery," encompassing the American South, Mexico, and the Caribbean region.

Other Pinkerton detectives included Hattie Lawton, who posed as Webster's wife. Warne was also said to be instrumental to Lincoln's safe passage to take the oath of office and in convincing Pinkerton that there was a plot to assassinate Lincoln in Baltimore. Harry W. Davies, another Pinkerton agent, also helped convince Pinkerton of the threat, and was credited with gathering and supplying information on possible plots.