After the return of the regiment from the Kilpatrick raid, in March 1864, Major Wells was detached and placed in command of the 7th Michigan Cavalry (which had lost its commander) for a month. He commanded a battalion of Sheridan's cavalry at the Battle of Yellow Tavern, in which J.E.B. Stuart was killed. Wells was promoted to colonel on June 4, 1864. From September 1864 to April 1865, he was several times in command of the Third Cavalry Division. In the Battle of Tom's Brook, Virginia (October 9, 1864), a cavalry action, Wells commanded a brigade of Custer's division, and at Cedar Creek, his brigade took a foremost part in turning the rout of the morning into a decisive victory at nightfall, capturing forty-five of the forty-eight pieces of artillery taken from Jubal Early's fleeing army.