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William ran away but not for long. After Abraham Bertolet's body had been carted off, he returned home. That was where he was on Monday morning, 22 June 1863 when District Attorney Enoch Banks, Sheriff Kile, Deputy Provost Marshal Edward Johnson and Eisenberry arrived to arrest him. Banks met with William and advised him to give himself up. William was about to do that when the other men showed up, scaring him and causing him to run off. The arresting officers would later tell the newspapers that his friends had helped him escape.
Two days later, on Wednesday, 24 June Provost Marshal Freedley sent twenty soldiers to find and arrest William, but they were unsucccessful. Instead, they arrested John Wampole, the town's storekeeper, Charles Hauck and Henry Graff. They were charged with aiding and abetting William with his escape on Monday and escorted to Philadelphia where they were held for further examination.
A few days later U.S. Commissioner Aubrey Smith held a hearing and questioned three witnesses: Deputy Provost Marshal Johnson and two citizens. All three testified that Wampole had tried to convince William to surrender. But, since Wampole spoke to William in German and the arresting officers were not familiar with that language, there was a misunderstanding about Wampole's intentions. All three men were subsequently released.
The soldiers remained in Perkiomenville, searching for William. On 7 July Freedley wrote to Provost Marshal General Fry that he had hired John Stauffer, the ex-sheriff of Montgomery County, to track down William. It was widely believed that William was being hidden by some of his neighbors. However, that was not the case. William had left Frederick Township since the large military presence made it difficult for him, as well as his neighbors.
On 13 July 1863, shortly after dark, William was captured in Allentown, PA, reportedly preparing to leave for New York with "one of his cronies." He had been spotted in a cigar store by someone who knew him and immediately informed the authorities. When he was arrested by Franklin Taylor, a police officer, William did not resist and he was unarmed. Taylor placed him in the Allentown jail and, to ensure he did not escape, attached a ball and chain. The next day he was placed on a train and sent to Norristown, arriving there at noon. He was questioned by Freedley before being sent to Philadelphia to await his trial.
In Philadelphia he was confined at the the headquarters of the provost marshal while U.S. District Attorney George Alexander Coffey tried to decide what to do with him. Both the army and the civilian authorities thought it was their duty to try him. It was finally decided that William would stand trial by court martial on the charges of desertion and murder. William was then transferred to Fort Mifflin in southwest Philadelphia.
Commissioned in 1771, Fort Mifflin was built on Mud Island, located in the Delaware River just below Philadelphia. It was used during the American Revolution and rebuilt during the War of 1812. During the Civil War Fort Mifflin was used to house Confederate prisoners of war, deserters and political prisoners. It was not a large complex and did not have any real place to house prisoners. There were three bomb-proofs, which had no ventilation other than their doors. They were accessed through one door opening into halls which led to them. Seventy-five army prisoners were confined in the first, fifty-eight political prisoners in the second, and eighty-two Confederate soldiers in the third.
The bomb-proofs were dark, damp and dirty. During the heat of the summer, the walls would sweat. It was here William waited for his court martial. Military law called for brief confinement and speedy justice. The accused was not to be imprisoned for more than eight days or until enough officers could be gathered for the panel.
That did not happen until 16 November 1863. After the charges were read, William requested a delay so he could try to locate a lawyer to represent him. Given the seriousness of the indictments, the court agreed and adjourned for a week. William tried to have Philadelphia lawyer Charles Hunsicker plead his case, but the lawyer declined. William was left to defend himself. He pleaded guilty to desertion, but not to murder.
When he made his statement to the court, he admitted that he had deserted as charged. He insisted that he had every intention of returning to his Regiment, but he did not, due to the influence of friends. As for the night of the alleged murder, unknown individuals had come to his house in the middle of the night. Any actions he took were to defend his home and family.
The courtroom was cleared and, after little delay, the panel returned and delivered the verdict. William was found guilty on both charges and he was sentenced to be hanged. He was shocked by the decision. He hoped that a review board would overturn the verdict. By the end of November, he was scheduled to be executed at Fort Mifflin on Friday, 19 February 1864 between noon and 2:00 P.M.
As the papers were sent through the channels, the judge advocate general's office was unhappy with the way the trial had been conducted and overturned the verdict due to "informality." William was hopeful that his ordeal would be over since military law prevented an officer or soldier from being retried for the same offense. However, he was not aware that when verdicts overturned, the prisoner could be recharged and tried again.
While William waited in the bomb-proofs at Fort Mifflin, in December, General Darius Couch, commander of the Department of the Susquehanna, appointed another court-martial board. On 15 February 1864, the new board met to begin the case of Private William H. Howe.
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