Gary Scharnhorst in The Life of Mark Twain: The Early Years, 1835-1871, (page 128) repeats the story of Sam aboard the last steamboat allowed through the Union blockade.
Benjamin Griffin has discounted this narrative . "It is often stated as fact that Clemens returned to Missouri on the steamboat Nebraska, which left New Orleans on 14 May and arrived in St. Louis on 21 May. This is conjecture, based, at several removes, on the official biography of Mark Twain by Albert Bigelow Paine (1861-1937). "
Griffin goes on to say "Paine's informant was surely Clemens, whose own accounts of his exit from the river are similarly incoherent". ...
Griffin further remarks that "The presumption that Clemens was aboard the Alonzo Child when she left St. Louis for New Orleans on 2 May has bred speculation on how he later got back to Missouri amid the disturbances of the war. As a matter of fact, we do not know with any assurance that he made the trip down at all. Will Bowen had left and gone home in April, and Clemens may well have followed suit."
Michael Marleau follows the original theory that Sam did return to New Orleans on the Alonzo Child. He takes the recollections of Horace Bixby seriously, that his former steersman Samuel L. Clemens, while on the steamer Alonzo Child in 1861 under Capt. DeHaven, had “kept turning the wheel until the war broke out. His boat was then in the south, and he piloted three months for the Confederacy. Then he got through the lines and went home.” Historical evidence, however, supports the fact that Clemens made it through the lines in May, a month or so after the beginning of the hostilities. Still, Bixby’s statement is unequivocal. Sam Clemens “piloted three months for the Confederacy.”
Marleau goes on to say Bixby's statement that Clemens “piloted three months for the Confederacy” is not the only statement he made concerning Sam Clemens at this time. “He was on board the Alonzo Child, was caught by the Confederates and had quite a time of it” and also “was caught in the blockade.” Up to now the Alonzo Child had no real difficulty getting through the blockade. The Alonzo Child would only be doing round trips between New Orleans and Memphis, but Clemens sought a way to St. Louis. This leaves several possibilities. The first possibility is that Clemens piloted the Alonzo Child to Memphis. By order of General Pillow the Alonzo Child was seized at Memphis and awaited the will of the Confederate authorities. Clemens would certainly have “had quite a time of it” as one of the pilots. However he accomplished it, Clemens left Memphis, not on the Alonzo Child, but on the Nebraska. A second possibility is that Clemens went to Memphis, already aboard the Nebraska, as an extra pilot.
The Nebraska was stopped. Inspection and questioning insured that the officers would have quite a time of it, and they were “sent to St. Louis and imprisoned in a tobacco warehouse on Washington avenue.” In this makeshift prison Clemens had few options, but upon giving his oath of allegiance to the Union he was eventually released. In St. Louis, Clemens roomed with his sister and brother-in-law William Moffett. His niece Annie Moffett later recalled that Sam spent some time there and was afraid to venture out.
From Fears:
May 14 Tuesday – Sam departed New Orleans as a passenger on the Nebraska. Commercial traffic was halted. This was the last boat allowed through the Union blockade at Memphis. Sam’s days as a river pilot were over, though he did not know it at the time. He would later wax nostalgic and eloquent about his idyllic career on the river. Just as his idyllic days of boyhood in Hannibal had abruptly ended, so too did his time on “the best job in the world.” Paine gives the name of the boat as the Uncle Sam: “I’ll think about it,” he said. “I’m not very anxious to get up into a glass perch and be shot at by either side. I’ll go home and reflect on the matter” [MTB 161].
May 21 Tuesday – Sam arrived in St. Louis. Sam hid out in the Moffett residence, fearful of being arrested by Union agents and forced to pilot a gunboat. He stayed there for a few weeks [MTL 1: 121]. During his stay he was invited to visit his cousin James Lampton, also in St. Louis. James was Jane Lampton Clemens’ first cousin, and the model for Colonel Mulberry Sellers in The Gilded Age. Sam stayed at James’ house for a few days. It was during this stay when the famous “turnips and water” dinner was served. When Sam came home one day he was given the key to the neighbor’s house, owned by George Schroter (or Schroeter) (1813?-1896?), Will Moffett’s business partner. The Schroter family was in Hannibal and it was thought Sam would be safer in their St. Louis house. One day a man who gave the name “Smith” came looking for Sam and his mother recognized him as a friend of Sam’s. The man came with the project of forming a Confederate company in the Hannibal area to join General Sterling “Old Pap” Price (1809-1867). Sam accepted and began the Marion Rangers fiasco [MTBus 60].
May 22 Wednesday – The Polar Star Masonic Lodge Number Seventy-nine of St. Louis initiated Sam Clemens an Entered Apprentice, the next step up [Jones 364]. Note: Strong gives May 21 for the initiation [88].
June 12 Wednesday – Sam was probably no longer hiding out at his sister’s, for on this date he was raised to Master Mason (second degree) in the Polar Star Masonic Lodge Number Seventy-nine of St. Louis [Jones 364].
June 15 Saturday ca. – The Missouri state government had fled from Jefferson City by this date. Absalom Grimes wrote in his memoirs that he, Sam Bowen and Clemens were in Hannibal and were ordered to report to General Grey in St. Louis. (This may have been General Henry Gray, Jr. (1816-1892) spelled “Grey” by Grimes.) They made the trip on the Hannibal City and were instructed to be pilots carrying soldiers up the Missouri River, in pursuit of Governor Claiborne Fox Jackson (1806-1862). The three escaped and returned to Hannibal [Dempsey 266-7].