Mortaigne became a leader of a large scale mutiny which paralyzed the Swedish army, demanding the immediate payment of their arrears. In July 1641, Mortaigne and Adam von Pfuhl were invited into Stockholm as representative of the mutineers. Mortaigne was promoted into brigadier general and received land in Pomerania, while the rest of the army was paid the sum of 486,200 thalers settling the crown's debts. During the course of 1642, Mortaigne took part in the second Battle of Breitenfeld and was later severely injured during an engagement in the vicinity of Brieg. In 1643, Mortaigne's forces ravaged through Moravia. On 12 February 1645, he was captured by an Imperial patrol outside Borna while carrying a portfolio of important documents. He was released on ransom, later commanding the Swedish center at the Battle of Jankau. In 1646, he returned to the Landgraviate of Hesse-Kassel with the approval of Christina, Queen of Sweden, receiving the rank of general-lieutenant. He led Hesse-Kassel's troops during the Hessian War. On 10 July 1647, a cannonball crushed his left leg, gravely wounding him while he was besieging the Rheinfels Castle.