On September 2, 1862, Abbott's regiment covered the retreat of the defeated forces of Union Major General John Pope after the Second Battle of Manassas or Bull Run. Weeks of hard duty took their toll on Abbott, who was not fully recovered from the wound he suffered at the Battle of Glendale. Abbott missed the Battle of Antietam because he was hospitalized with typhoid fever and grief over the death of his brother at Cedar Mountain. The 20th Massachusetts Infantry again suffered heavy losses at Antietam. Soon after the battle, Abbott's brother Fletcher, who was suffering from dysentery, joined him in the hospital. Abbott recovered by November 1862 and returned to the regiment camped at Falmouth, Virginia across the Rappahannock River from Fredericksburg, Virginia. He was accompanied on his return by Holmes, who was returning after recovery from a wound suffered at the battle of Antietam.