President Lincoln's passage through Annapolis en route to and from the Hampton Roads Conference in February of 1865 is a little known event. It is sometimes mentioned briefly in books on Lincoln or the Civil War. There are also sketchy details in contemporary newspaper accounts (though there are no surviving newspapers from Annapolis for the dates Lincoln was here).
There are probably a number of reasons so little is known about Lincoln's time in Annapolis. First, as noted, there are no Annapolis newspapers for that period. We do have "The Crutch," which was the weekly sheet published at U.S. General Hospital Division 1 on the grounds of the Naval Academy. This little paper gives a couple of sentences noting Lincoln's appearance at the wharf and that the hospital band serenaded him as he boarded the Thomas Collyer.
Second, Lincoln was not here very long. The contemporary newspaper accounts we do have generally agree that he arrived here at about 1:00PM on Thursday, February 2, and that he had departed on the steamer Thomas Collyer by about 1:45PM. When Lincoln returned on the 4th there was a special train waiting at the Naval Academy wharf to return the presidential party to Washington. So Lincoln's total time in Annapolis was probably less than an hour over two separate days.
Third, Lincoln had only decided to make the trip at 9:00AM that morning after reading Grant's telegram. Within 2 hours he was on the train for Annapolis with almost no one in his own cabinet--let alone the capital--even knowing he was gone. One of Lincoln's secretaries, Edward Duffield Neill, had this recollection: "On the morning of the 2d of February, 1865, between nine and ten o'clock, as I was ascending the stairs to the second story, to reach my room, I met Forbes, an intelligent servant, descending with a small valise in his hand, and I asked, 'Where are you going?' Looking up to see no one was near, he whispered, 'Fortress Monroe,' and hurried on. When I reached the upper hall I met the President with his overcoat, and going to my room, looked out of the window, and saw him quietly walking around the curved pavement which leads to Pennsylvania Avenue, while Forbes was following, at a distance of two or three hundred feet, as his valet. Waiting for some time, I then crossed the hall to the room of the principal secretary, Mr. John G. Nicolay, and quietly said: 'The President has left the city.' 'What do you mean?' he asked; and I replied: 'Just what I have said.' Rising quickly, he opened the door which communicated with the President's room, and was astonished to find the chair of Mr. Lincoln vacant." (Wilson, Ruffus Rockwell, "Intimate Memories of Lincoln," p. 601).
Fourth, Lincoln may have been trying to avoid distracting the Maryland Legislature from its consideration of the 13th Amendment to the U. S. Consitution. Secretary of State William Seward, also on his way to the peace conference in Virginia, had passed through Annapolis on February 1st--the day before Lincoln--and had brought with him and hand-delivered to Maryland Governor Augustus Bradford the amendment abolishing slavery which Congress had finally passed on January 31st. Seward had urged Bradford to convene the legislature and have them ratify the amendment, apparently hoping to have it done before he continued on to Virginia. The House of Delegates did promptly ratify it but the Senate referred the amendment to its committee on Federal Relations. Thus it was still under consideration on February 2nd when Lincoln walked within sight of the State House dome. He certainly would have known that Seward had carried the amendment to Annapolis the day before and, assuming he believed it to be then under discussion, Lincoln would not have wanted to disrupt those proceedings.
Fifth, Lincoln was never one to draw attention to himself anyway, and in passing through Annapolis he was intent on getting to Ft. Monroe as quickly as possible. Still, it must have been hard for him to literally walk through a military hospital and not stop to say something to the soldiers recovering there.
It has been suggested by some that probably Lincoln hurried through Annapolis because it was filled with Southern sentiment and in walking through town he was exposing himself to great danger. This is simply not something I can believe. Annapolis, by 1865, was a major Union hospital, supply depot, and transportation hub. The army was everywhere. This theory is further refuted by Lincoln's own well known disregard for his personal safety (a trait which would finally catch up to him 10 weeks later). When President-elect Lincoln was on his way to Washington in 1861, advisers convinced him to sneak through Baltimore because of threats of assassination. The threats were credible but Lincoln was criticized and mocked quite severely in the press. It probably saved his life but he regretted ever after this stealthy passage through Baltimore. There is no way he would have repeated that, at least for safety reasons, in Annapolis in 1865.