After the beginning of the Second World War, Wäger was the commanding general of the XXV Army Corps.

From 6 November 1939 to 23 December 1941, he led the XXVII Army Corps in the West.

XXXIV on the central section of the Eastern Front, which was defeated in the Battle of Moscow.

He was transferred to the Führerreserve in early January 1942 and finally retired in August 1942.

Wäger settled in Baden-Baden and in the last days of the war was able to hand over the city to the advancing French without a fight.