After the Battle of Fredericksburg, Meagher and his men returned to the battlefield to retrieve the bodies of fallen comrades. They found Major William Horgan, a key figure in the Irish Brigade, dead. Meagher ensured Horgan's body was embalmed for transport back to New York.

In 1863, Lincoln faced increasing pressure compounded by personal tragedy with the death of his young son, Willie. The Union Army at Falmouth suffered high desertion rates, sickness, and poor conditions. Meagher developed a severe knee infection, prompting him to take medical leave. He brought Major Horgan's body back to New York and arranged for it to be displayed at the Irish Brigade headquarters—a sight that dampened recruitment efforts.

Despite the Emancipation Proclamation, which brought hope and jubilation to enslaved people, Black Americans, and abolitionists, the Irish community was increasingly disillusioned with the Union cause. Meagher tried to rally support but faced resistance. Lincoln's dismissal of General McClellan further unsettled the Irish Brigade, though the arrival of General Joseph Hooker lifted spirits slightly as he improved conditions in the camp.

In February 1863, Meagher met with Lincoln to request time for the brigade to recover and for promotions for deserving officers.