Lt. Colonel Fairchild's wound was in his hip and was so severe that he had to be sent back to Wisconsin for surgery and recuperation. Colonel Allen's wound was in his arm, and he was able to recuperate with the Regiment as they stationed in the vicinity Pittsburg Landing. On May 1, he led the regiment to the vicinity of Corinth, Mississippi, and participated in laying siege to that city. During the siege and for some months after, their superior, Brigadier General John McArthur was elevated to command of their Division, and thus Colonel Allen was elevated to command of the brigade, and Major Reynolds was left in command of the 16th Wisconsin. After the successful taking of Corinth, Colonel Allen's brigade was engaged in maneuvers against Confederate forces still in the area, but before they could concentrate, another force of Union soldiers encountered the enemy at Iuka. After Iuka, it became apparent that the enemy was concentrating for another push toward Corinth. Allen's brigade returned there and formed a defensive position. At this Second Battle of Corinth, they again conducted orderly retreats to strong defensive positions, then repelled waves of Confederate attackers.