After the Battle of Chancellorsville, Pettit resigned from the service for medical reasons and returned home. He remained there for about a year before rejoining the army in March 1864. This time he was with the U.S. Veteran Reserve Corps, a branch of the service for veterans not fit for active field duty. He was assigned to Company F of the 12th Regiment.

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On July 20, four months into his service with the Veteran Corps, Pettit was made superintendent and inspector of Union military prisons in Alexandria, Virginia. Sometime after that, his troubles began, and a year later, he was arrested and charged with 'conduct to the prejudice of good order and military discipline,' a blanket charge that essentially covered three separate, major alleged incidents. It seems that Pettit was on a self-directed mission to expose deserters from the Union army–not an easy task considering that prisoners frequently were sent to military prisons without any record of their offenses. Pettit was so obsessed with his mission, his accusers said, that he tortured 'confessions' out of men. He of course denied the allegations against him and pled not guilty. After four months of legal delays that followed his arrest, he finally came to trial November 14, 1865, before a court-martial board chaired by Brevet Major General George S. Greene.

The trial opened with Dewitt James taking the witness stand to describe the first alleged incident: Pettit kicking the old man in the face at Washington Street Prison. The vivid description was damning, but Pettit had an explanation: James was lying. In cross-examining James, Pettit said the commandant had a vendetta against him because he had fired him from his post and court-martialed several of his men. James replied that his only animosity toward Pettit was based on his confining men in the Alexandria Slave Pen, the crude prison where slaves were kept before sale. Pettit accused James of complaining about him to Lafayette Baker, chief of the Federal Secret Service, and others. James retorted that these men had approached him to solicit his opinion, because under Pettit's supervision, the Alexandria prisons had grown notorious for their scandals.

After James's testimony was finished, the prosecution called Sergeant Hiram Belknap of James's regiment. Belknap confirmed James's story of the bloodied old man, adding that as Pettit tightened the chain that pulled the man's wrists toward the ceiling, he yelled, 'That is the way I want you to tie up men!' Belknap continued with a description of the scene that suggested this was not the only time Pettit had tortured prisoners. 'The old man's toes barely touched the floor,' Belknap said, 'but when Captain Pettit was gone, we'd give the prisoners a bucket to stand on. I saw the blood run from the man's nose and mouth.'

The second alleged indicent occurred at Princess Street Prison, where Pettit was accused of stringing up one Caleb Smith, alias Caleb Sweet, much as he had done to the old man at Washington Street Prison–but for up to 12 hours at a time. Pettit allegedly did this about half a dozen times before Smith finally gave in and 'confessed' to being a deserter. It is unclear whether Smith had ever really been in the army or whether he was simply trying to avoid further pain.

The prosecution called a string of witnesses to support its charge. The first was Sergeant Michael Murray, who was at Princess Street Prison from June 1864 to May 1865. 'Sometimes he [Smith] could hardly speak,' Murray testified, 'and he lost the use of his limbs.'

Another witness, Joseph Bannister, was originally disqualified from testifying because of a prior conviction for deserting from the 106th Pennsylvania Infantry. After some legal maneuvering, however, he was allowed to tell his tory. 'I was six months in the Princess Street Prison,' he testified. 'I well recall Caleb Smith, alias Sweet. He was tied up eight or ten times, for as long as 16 hours each time. Captain Pettit said, 'I will make him own up or put him in his coffin.' I saw Sweet tied up in pouring rain and in the hot sun, with blood oozing from his ears and flies picking his eyes.'

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