During the siege of Charleston Harbor Stevenson commanded the 3rd Brigade in Alfred H. Terry's division. He remained in brigade command around Charleston until January 1864. On April 19, 1864 he was placed in command of the 1st Division, IX Corps. Stevenson had previously fought alongside many of the men from IX Corps in North Carolina. Now, he was one of Burnside's ablest division commanders. He led his new division into action at the battles of the Wilderness and Spotsylvania. On May 10, 1864 while resting beneath a tree, Stevenson was shot through the head by a sniper's bullet. His body was returned to Massachusetts where he was buried at Mount Auburn Cemetery in Cambridge.