In 1852, Haydon worked as a resident engineer on the construction of the Orange and Alexandria Railroad middle section and Warrenton, Virginia.
[12] On October 15, 1861, Major Jeremy Francis Gilmer who would later become famous for his defense of Atlanta, Georgia replaced Lt. Dixon and led the construction efforts at the fort.
Writing after the battle, capture and release of paroled prisoners, a number of officers commented on Haydon's role in the defense of the fort.
Colonel Adolphus Heiman of Army of Tennessee commended Haydon as one of a cadre of Confederate officers (including Major J. F. Gilmer and Captain Miller fellow engineers) who deserved particular credit for their management of the fort's guns.
"[13] Haydon was paroled for the first time in November 1862 at Aiken, South Carolina[10] Following his parole in late 1862, Haydon reported to Col. Walter Stevens in the Department of Richmond and worked on rebuilding the Pocahontas bridge over the Appomattox River near Petersburg, Virginia as well as performing reconnaissance on the Potomac river near Point of Rocks, Maryland.
[11] [16] Haydon became chief engineer for the Edisto and Ashley Rivers canal company in South Carolina in 1866 as part of a scheme to provide the city of Charleston with a fresh water supply.
This left chief engineer William Milnor Roberts with the task of locating over 600 miles of railroad in Western Dakota and Eastern Montana [11] what was known at that time as the "middle division" of the Northern Pacific.
[11] Muhlenberg, however, didn't return until November 28, where the military escort under Captain Edward Ball reported 57 soldiers injured by freezing weather.
On July 23, 1872, Haydon led the railroad survey party from Fort Ellis, a United States Army fort, east of present-day Bozeman, Montana, consisting of Haydon, chief of party, two principal assistants, in charge of the compass and level, together with rodmen, chainmen, and others (altogether 20 men).
[11] Haydon supply train consisted of almost seventy wagons with rations for 105 days and a small herd of beef cattle.
[23] The survey party and military escort proceeded without the benefit of Crow Indian scouts, largely due to rumors of a Sioux-Cheyenne attack or preparations for multiple river crossings with ferry boats.
[11] On August 13, there were as many as two thousand lodges of Lakotas, Cheyennes, Arapahos and Kiowas gathered on the Powder River under Sitting Bull, Red Cloud and Crazy horse.
After performing an annual sun dance ceremony,[24] a war party was formed with as many as a thousand warriors to go upstream on the Powder to locate and fight their enemy, the Crows.
[11] The peace treaty of Fort Laramie of 1868 was still in effect, but Sitting Bull found himself just miles from hundreds of horses and cattle and the railroad surveyors led by John Haydon.
During the battle, Sitting Bull, in a personal show of bravery, took four others with him to within two hundred yards of Baker's forces and sat down with pipe and tobacco.
Although they continued on until August 18, at time, Haydon, exhausted and apprehensive about the safety of the survey party from raids as well as knowing his work with the railroad was ended, requested Baker to return to Fort Ellis.
[11] With Haydon resuming as party chief, the surveyors reached the south fork, 20 miles west of Harlowton, Montana, on September 15.
Over the next two weeks, marching through snow and bitter cold, Haydon's party crossed over the pass separating the Mussellshell from the Missouri River by way of Sixteen Mile Creek.