In August of 1865, Emily petitioned the court for a divorce from Halcyon. Emily also asked the court to prevent Halcyon from selling land or property since if he did so he would be able to leave the state and avoid paying alimony to Emily. This second request was granted in August 1865. In her petition, Emily stated that:

...on or about the 4 day of July 1862 ...Halcyon G. Bailey became and ever since continued to be by the immoderate use of intoxicating liquors grossly and habitually inebriate and during the last three years the said Halcyon G. Bailey has been guilty of intolerable cruelty to the petitioner, and during the time last aforesaid he has repeatedly injured and shamefully maltreated her 
And... has repeatedly, since said intermarriage,... used the most gross and indecent language towards her, and has applied the most vile and insulting language to her, and exhibited a total want of affection for her, all which acts... have wholly destroyed her happiness and defeated the purposes of the marriage relation.