Allen returned to Pittsburgh in 1855 after three years out west. In July 1857 he married Elizabeth Robinson and together they raised five children. The outbreak of the Civil War found Allen constructing a railroad in today's West Virginia. He and his family were seized by Confederate forces and held captive until repatriated at Washington, D.C. He immediately offered his services to his friend, General McClellan, now commander of the Army of the Potomac. Circumstances instead took Allen to Virginia's Shenandoah Valley where he fought in the battles of Lewisburgh and Cross Keys. Allen later became a colonel in the 155th Pennsylvania Volunteer Infantry Regiment and fought at Fredericksburg and Gettysburg. He was medically discharged after Gettysburg but continued in a civilian role to provision the Union army in the Shenandoah Valley. (Allen's military history may be found in "Under the Maltese Cross.")