Arrested by Secretary of the Navy Gideon Welles in November 1865, Rear-Admiral Semmes of the Alabama was simply charged with not surrendering himself to his enemy after his ship was disabled, though the latter had left him to drown. Semmes was rescued from the sea by the English yacht Deerhound, taken to England, and eventually made his way back to Richmond to serve the American Confederacy once again.
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North Carolina War Between the States Sesquicentennial Commission
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Prison Diary of Raphael Semmes
"At the close of the Civil War many of the Confederate leaders were arrested and imprisoned. [Returning to the CSA after losing the Alabama and made a brigadier-general at Danville, Rear Admiral Semmes] was subsequently paroled under the terms of the Johnston-Sherman convention of April 26, 1865.
Diary: On the 15th of December, 1865, whilst sitting with my family, a lieutenant of marines and two sergeants entered my house, having first surrounded it by a guard of some 20 men, and presented me with an order for my arrest from the Secretary of the Navy . . . dated 25 November 1865.
[27 December]: Reached our dock [at New York . . . Breakfasted with [General Jubal] Early on the morning of the 28th.
[28 December]: Taken to headquarters of colonel of marines and thence to the navy yard, where I was put in close confinement in the dispensary . . .
[4 January]: Judge [James] Hughes has had an interview with the President in my case. My arrest was by a cabal of the cabinet, unknown to the President.
Tuesday, 16 [January]: The ground is covered with snow this morning . . .The unfinished Washington monument, speaking of the ingratitude of the nation is seen nearly in the same direction with Lee's mansion and the dome of the capitol, and the latter flaunts the flag, the old flag made new by the war, which daily covers in their deliberations the faction of the Rump Congress which daily and hourly proclaims the Southern States to be conquered provinces and refuses admission to her representatives.
My newspaper is brought in with my breakfast. It is the National Intelligencer! But how changed from the days of Clay and Calhoun! I read in it sometimes such a paragraph as this: "Trial of Raphael Semmes. (It does not even call me the late admiral, or the so-called admiral, or the so-called late admiral of the so-called late Confederate States), "late commander of the rebel steamer Alabama, it is generally believed, will take place very shortly.
I do not think I will be speedily tried. This would not be in accordance with the Bastille system imported from a by-gone age and the French Revolution . . . Nor do I think that I shall be tried at all, as the Government has no case and can make none, though it is even now scouring the "mappings" of Northern commercial cities for evidence against the pirate. N'importe. I shall be punished.
[Friday, 26 January]: The Yankees have are getting the people by the gills; they have passed the bill enlarging the functions of the Freedmen's Bureau. Silly people! They fancy that they are governing themselves.
[Saturday, 3 March]: [Pendleton] Colston came over to-day. Saw the Secretary of the Navy [Gideon Welles] . . . Mr. Welles admitted that I had been confined too long, but that it had not been his fault. He regretted, he said, that I had returned to the country; a good deal of trouble might have been saved if I had not done so! Humane man!"
(The Prison Diary of Raphael Semmes, Elizabeth Bethel, Journal of Southern History, Volume XXII, Number 4, November 1956, pp. 498-499, 502-506, 509)