In 1828, as he was returning to St. Louis, Missouri from the 1828 rendezvous, he died near Scotts Bluff, Nebraska. The bluff was named in his honor. The story of how he died has several versions but he was apparently too ill to travel and was abandoned by his companions. His bones were found the following season many miles from where he had been deserted.

The story of his Scott's death was first recorded by Warren A. Ferris, an employee of the American Fur Company, who traveled through the area in 1830. He related that during Scott's eastward journey, he had contracted a severe illness. Two comrades placed him in a boat and attempted to transport him downstream. However, for some unknown reason, the two men abandoned Scott on the north bank of the Platte River. The next spring, Scott's skeleton was found on the other side of the river, implying that he had somehow managed to cross to the opposite bank before he died.

A subtle variation on this story was recorded two years later by Washington Irving. Instead of being abandoned by just two men, the ailing Scott was supposedly left behind at the Laramie Fork by a larger party who feared for their lives due to starvation. The next summer, Scott's bones were found near the bluffs - 60 miles from where he had been left to die.

In 1834, missionary Jason Lee recorded a story about Hiram Scott that was very similar to those earlier versions, except that the pathetic Scott had traversed 100 miles before dying near the bluffs on the North Platte River.

The story of what happened to Hiram Scott was told and retold over the years, with more variations. Some stories included dramatic attacks by Indian warriors while others suggested murder and foul play. Some stories include the noble theme of the doomed Scott insisting that his comrades leave him behind so they might save themselves from his fate.

There has been some speculation that Hiram Scott was actually injured in an encounter with some Blackfoot Indians that took place at the 1828 rendezvous at Bear Lake, Utah. This has been used to explain why Scott became incapacitated on his journey back east, but as with most of the information about Hiram Scott, very little is known for certain.

Though history has become hopelessly confused, research has proved that there was a Hiram Scott prominent in the Rocky Mountain fur trade from 1823 until 1827; and that he disappeared in 1828 and was never heard from again. His companions remain unidentified, but research strongly suggests that William Sublette was the leader of the 1828 caravan, who issued instructions to these men to remain with him. It was also William Sublette who led the springtime caravan of 1829 that discovered Scott's skeleton, miles away from the spot where they reported he had died.