At the outbreak of the American Civil War, Allen was one of the first Wisconsin volunteers to sign up for service in the Union Army. He helped organize a company of volunteers, known as the "Miners' Guards", and was elected captain. His company was then enrolled as Company I of the 2nd Wisconsin Infantry Regiment.[4]
The regiment mustered into federal service in June 1861 and went east to Washington, D.C. Shortly after arriving, they were assigned to the brigade of William Tecumseh Sherman and went south into northern Virginia with the Manassas campaign on July 16. Within days, they were engaged at the disastrous First Battle of Bull Run. The 2nd Wisconsin Infantry was with Sherman's surprise attack on the Confederate right flank which briefly destabilized the Confederate line. After the Union retreat from Virginia, Allen was promoted to major, in place of Duncan McDonald, who resigned.[4]
In December 1862, Allen was promoted to colonel and assigned to take command of the 5th Wisconsin Infantry Regiment, to replace Amasa Cobb, who had been elected to Congress.[6][7] He reported for duty and took command of the regiment on January 26, 1863.[8]
He led the regiment at the Battle of Chancellorsville in the Spring of 1863, where he performed his most notable war service. He personally led five companies of his regiment to storm the position known as "Marye's Heights". Nicknamed the "slaughter pen", 5,000 Union men had died in the previous assault on the position during the Battle of Fredericksburg. It was a steep hill topped with fortifications, with neighboring hills capable of supporting the defense by strafing any assault from the sides.[8]
Allen addressed his men to encourage them before the assault, saying:
Boys! You see those heights! You have got to take them! You think you cannot do it; but you can! You will do it! When the order 'Forward' is given, you will start at double quick—you will not fire a gun—you will not stop until you get the order to halt! You will never get that order!
— The Military History of Wisconsin (1866)
Allen led the assault through a barrage of bullets and chaff. As ordered, they ran up the hill without firing their weapons, then bayoneted men in their fortifications. They captured the heights, and accepted the surrender of the Washington Battery of New Orleans, with the enemy colonel complimenting Allen for his daring and the bravery of his men.[8] The assault in the neighboring sector failed to secure their position, so Allen then led his men to assault that area from behind, capturing it. In all, Allen's assault captured nine cannons, over a hundred Confederate prisoners, and a comparable number of rifles, muskets, and other small arms.[8]
Despite their gallant effort, the Battle of Chancellorsville was another disaster for the Union, and they were soon forced to abandon the heights and return to the north side of the Rappahannock River.[8] Following Chancellorsville, the Confederate Army went on the offense into Union territory, on the campaign which culminated in the Battle of Gettysburg. The 5th Wisconsin Infantry, then part of VI Corps, arrived late on the second day of the battle and were largely held in reserve after they arrived.[8]
Shortly after the battle, the 5th Wisconsin was ordered to go to New York City to assist with the draft riots. They were stationed in New York until October, when they returned to VI Corps in Virginia.[8]
In November, the 5th Wisconsin was again selected for a special assault—along with the 6th Maine Infantry Regiment—when they were assigned to seize the Confederate outpost at the Second Battle of Rappahannock Station. Allen again led his men in a successful assault on the fortifications, but Allen was shot through the hand during the battle, rendering him unfit for duty.[8] While recuperating, he returned to Wisconsin where he spoke at several events to support the Union cause and veterans charities.[9] Around that same time, Allen re-enlisted as a veteran along with about 200 of his regiment. Their 200 veterans were not enough to qualify the regiment as a veteran regiment and remain in service, so the regiment would disband at the end of the enlistment term in August 1864.[8]
Allen returned to Virginia with the regiment in March 1864, but his health remained somewhat delicate after his recent wound. Shortly after returning, he was assigned to a special commission in Washington, D.C., to examine officer candidates for the United States Colored Troops and he served there until the end of the original term of enlistment for the 5th Wisconsin Infantry.[10]
5th Wisconsin Infantry (Reorganized)
About the time of the expiration of the 5th Wisconsin Infantry, Allen decided he was well enough to return to service.[11] Governor Lewis authorized the reorganization of the 5th Wisconsin Infantry in Wisconsin and reappointed Allen as colonel. Allen raised and organized seven new companies of volunteers and quickly marched them back to Virginia to integrate with the veteran remnant battalion of the old 5th Wisconsin.[8] Upon rejoining VI Corps at the Siege of Petersburg, Allen was placed in command of a brigade.[8]
In this role, Allen led one final assault of the war, charging the enemy's works at the Third Battle of Petersburg. The 5th Wisconsin Infantry was the first to enter the enemy's trenches, capturing several prisoners as the Confederates attempted to withdraw from the city.[8] They then joined the pursuit of Lee's army in the Appomattox campaign, and were responsible for the capture of Lieutenant General Richard S. Ewell.[8]
After Lee's capture, the regiment returned to Richmond, then mustered out on June 20, 1865.[8] Allen was nominated for an honorary brevet to brigadier general on January 13, 1866, and his brevet was confirmed by the U.S. Senate on March 12, with an effective date of March 13, 1865.[1]
After the war
Allen was the Republican Party candidate for Secretary of State in the 1865 election, running alongside Republican gubernatorial candidate and fellow Iron Brigade veteran, Lucius Fairchild. Both Republicans won their elections and were subsequently re-elected in 1867. Allen served as the state's ninth Secretary of State, from January 1866 through January 1870.
After leaving office, he moved to Oshkosh, Wisconsin, and became the publisher of the Oshkosh Northwestern newspaper. He ran the Northwestern until 1884. He then published a German language paper, the Wisconsin Telegraph until 1902.
Allen died of heart failure at his home in Oshkosh on December 12, 1905.[12] He was buried at Riverside Cemetery in Oshkosh.[1][2]