Muir was wounded at Maguaga, but recovered to lead the main body of the 41st at the Siege of Detroit. Later in the year, Muir commanded another detachment sent to aid the Indians attacking Fort Wayne, Indiana. The attack failed, but Muir retreated successfully to Detroit. During the following year, he took part in the Battles of Frenchtown, Fort Meigs and Fort Stephenson. He was one of several officers who became critical of the leadership of the commander of the division, Major General Henry Procter. Finally, he was taken prisoner at the Battle of Moraviantown, when the by now starving and demoralised 41st Regiment gave way before a charge of Kentucky mounted riflemen.