After three days at Cairo, he and his men crossed the Mississippi and marched to Benton, Missouri and from there accompanied General Pope to New Madrid. He was conspicuous during the 10-day siege, eventually assuming command of a brigade to capture the Upper Fort. During the battle, he led Companies A and B of the 5th Iowa Regiment and three companies of the 39th Indiana Regiment which fought gallantly. Following the surrender of "Island No. 10" on April 7, Worthington was again absent while his regiment were conducting operations in the area. He sailed to Hamburg Landing on the Tennessee River joining Pope's forces prior to the siege of Corinth. It was in the early morning hours of May 22 that, while in performing his duties as general officer of the day, that he was shot and killed by a sentry.