Though Taft promised he would keep her secret, he discussed her with several other officers and rumors soon spread around camp. Within two months it was no longer a secret that there was a woman among them.
In January 1862, Taft was court-martialed for conduct unbecoming an officer and a gentleman, including inducing Harriet Merrill to "don the habiliments of a male, that she might enlist." Though he was found guilty of other charges, including stealing, marauding and lying, he was not convicted of persuading Merrill to become a soldier, as it was clearly her idea.
Merrill was discharged prior to Taft's court-martial but was allowed to testify. She under oath that she "performed all the duties that the rest of the soldiers did."