General Aguirre moved to the deserts of the southeastern portion of the state and defeated the French forces in Parral, led by Colonel Cottret. By the middle of 1866, the state of Chihuahua was declared free of enemy control; Parral was the last French stronghold within the state. On June 17, 1866, President Juárez arrived in Chihuahua City and remained in the capital until December 10, 1866. During his two years in the state of Chihuahua, President Juárez passed ordinances regarding the rights of adjudication of property and nationalized the property of the clergy. The distance of the French forces and their allies allowed the Ministry of War, led by General Negrete, to reorganize the state's national guard into the Patriotic Battalion of Chihuahua, which was deployed to fight in the battle of Matamoros, Tamaulipas against the French. After a series of major defeats and an escalating threat from Prussia, France began pulling troops out of Mexico in late 1866. Disillusioned with the liberal political views of Maximilian, the Mexican conservatives abandoned him, and in 1867 the last of the Emperor's forces were defeated. Maximilian was sentenced to death by a military court; despite national and international pleas for amnesty, Juárez refused to commute the sentence. Maximilian was executed by firing squad on June 19, 1867.

Where did Aguirre defeat the French forces?