When the Civil War broke out, the "Hartford" was ordered to return home. Greene, having been promoted to lieutenant on August 31, 1861, arrived in Philadelphia on December 2, 1861. After a short leave, he volunteered for duty on the "Monitor". Greene was appointed executive officer, serving under Commander Lieutenant John L. Worden during its historic four-hour battle at Hampton Roads, Virginia, with the Confederate ironclad warship on March 9, 1862. During the battle he assumed full command of "Monitor" when Worden was temporarily blinded by shell fragments from an explosion from one of "Virginia"s broadsides. After the subsequent retreat and assessment of all damage Greene ordered the return to battle and continued engaging the "Virginia" to a standoff. Greene continued to command the "Monitor" until Thomas O. Selfridge, Jr. took command on March 10, 1862.