The 39th was tasked with guarding the Baltimore and Ohio Railroad. On January 2, 1862, the company met Major General Stonewall Jackson's Valley District Army (15,000 soldiers), but managed to retreat after a skirmish. Mann's decision making during the retreat earned him a promotion to lieutenant colonel. He served on the staff of General Alpheus S. Williams until leaving to join his regiment at the First Battle of Kernstown. The unit then moved to South Carolina and the 39th took part in the Siege of Fort Wagner; Mann sent the announcement of its capture to General Quincy Adams Gillmore.