After the 21st Massachusetts was transferred to Northern Virginia in July 1862, the regiment eventually became part of the Army of the Potomac and took part in several of the largest battles of the war including Second Bull Run, Antietam, and Fredericksburg. The regiment suffered its worst casualties during the Battle of Chantilly on September 1, 1862. In the confusion of the battle, fought in thick woods during a thunderstorm, Clark became separated from his regiment and wandered the Virginia countryside for four days before finding the army again. While he was missing, he was incorrectly listed as killed in action and an Amherst newspaper printed his obituary under the headline, "Another Hero Gone."