General Joseph E. Johnston commanded all Confederate forces in Virginia from 1861 until late in May of 1862. His initial post had been at Harpers Ferry, thought to be the key to the defense of the Shenandoah Valley. Johnston, however, believed that Harpers Ferry was indefensible, and that, in fact, Winchester was the key to the Valley. In June 1861, he evacuated Harpers Ferry and fell back to Winchester, which he began to fortify. Winchester's proximity to Manassas proved the wisdom of Johnston's move; the transfer of his command to Manassas was instrumental in the great Confederate victory of July 21, 1861.
Meanwhile, Johnston's engineers continued the fortification of Winchester. Among their first projects was the construction of Fort Collier, commanding the approach to Winchester from the north on Martinsburg Pike. Lieutenant Collier directed the work. Some federal prisoners may have worked here alongside Confederate soldiers. Collier and William Henry Chase Whiting chose the high ground occupied by the Stine Farm for the field fortification that was to bear Collier's name. The Stine House, built in the 18th Century, did not survive the Third Battle of Winchester. The present house dates from 1865-1867.
Only one eyewitness account of the fort's construction has come down to us. Harriet H. Griffin, a young Winchester girl, visited the fort on August 21, 1861. In her diary entry for that day, she describes what she saw:
"I have this day visited the breastworks or fortifications on the Martinsburg Pike with Father and Johnie. Was exceedingly interested. First work of the kind I'd ever seen. The first time I was ever so near a cannon. I looked into them. The cannon balls weigh 42 pounds each. There were four cannons planted and much ammunition there. A great many men were working [and I] saw the magazines. They have several rifle ports which seem so secure. I have read of them, but have never seen them. They had several masked batteries. It seams real strong and well built. There is a high embankment of sand bags, barrels, and brush covered with dirt, part sodded over. They intend to sod it with a big ditch on the lower side. They have completely surrounded Stine's House which is now occupied by soldiers, some of whom were working there, some cooking, some washing, some on guard, and some lounging and some sleeping... Surely it is something to be remembered but I hope it will never be used."
Three months after Harriet Griffith's visit, the Confederate government in Richmond transferred General Thomas J. "Stonewall" Jackson to Winchester, Jackson, hero of the First Battle of Manassas, was as convinced as Johnston of the importance of Winchester, and of the Valley. "If the Valley is lost," he said, "Virginia is lost."
Jackson's force was too small to prevent General Nathaniel P. Banks' force from occupying Winchester on March 12, 1862. There was no fighting at Fort Collier in Jackson's Valley Campaign victory of the First Battle of Winchester on May 25, 1862, or in the Confederate victory in the Second Battle of Winchester on June 14-15, 1863. Until the fall of 1864, the fort saw the passing of troops up and down the Valley Pike, but no combat. The Stine Farm, within the earthworks, remained untouched by war, until the Third Battle of Winchester, on September 19, 1864.