Fort closed his Austin County, Texas law office for the duration of the war in June 1861 and paid his own travel expenses to join J.E.B. Stuart's cavalry in Virginia for the First Battle of Manassas. He was captured in Tennessee following the Battle of Farmington in May 1862, but escaped by leaping from a Union prison steamboat into the Mississippi River. Later, he created "Fort's Scouts," a small unit of Confederate Cavalry, acting in concert with General Nathan Bedford Forrest. By the end of the war he had served with the Confederate units in Texas, Virginia, Mississippi, Tennessee and Missouri. He was wounded during the closing weeks of the war. His unit surrendered about one month after General Lee's surrender.