The following information was taken from, "The Siskiyou Line" by Bert and Margie Webber. The book is available on Amazon here.
In 1855 Jefferson Davis, Secretary of War, gave orders to Lt. Robert Stockton Williams and Lt. Henry Larcom Abbot to form a party to survey a railway route from California to Portland, Oregon. They were to explore both the Deschutes Route and the Willamette Valley Route.
The route that Lt. Williams took would later become known as the Natron Cutoff (the route found in Maple Leaf Track's... Cascade Crossing route).
Lt. Abbot traveled north along the Deschutes Route. He was soon notified about an Indian war starting. By the time he reached Portland, he was informed that Williamson had already caught a steamship for San Francisco. From there, Williamson would survey a route that would connect with the railroad at Salt Lake City.
Abbot and his party headed south. Upon reaching the Umpqua River at Winchester, he learned that due to Indian hostilities, only large parties were able to make it through to Fort Lane on the Rogue River. He received an Army escort from Roseburg south through Cow Creek Canyon to Wolf Creek. The escort left them there to chase after Indians.
From there they were later escorted to Fort Lane, arriving on November 3rd of 1855. They then traveled south along Bear Creek through the Rogue Valley. After crossing into California, they continued to Fort Redding where they met up with Lt. Williamson.
The two were ordered back to Washington in January of 1856.
The image at the top of this page shows a train crossing Wall Creek Trestle. It stands 180 feet high and the actual route climbs at an impressive 3.38% grade there. The trestle has been photographed perhaps more than any other location on the route.
The south end of Tunnel 13 is the site of "The Last Great Train Holdup." In 1923 the three De Autremont brothers stopped and robbed the train. They killed the crew and in dynamiting the mail car, they killed a Federal employee. This brought in the FBI. The three were later caught and sent to prison. Watch this episode here on Oregon Public Broadcasting.
I don't think I'll end telling you about the route's history. Perhaps this will leave you curious enough to purchase a copy of "The Siskiyou Line." In it there's page after page of well written and quite interesting history. It also has a great number of pictures taken along the route. If you have an interest in the Siskiyou route, this is perhaps the best book available.