Personal disputes and later years

While Cope and Marsh dueled for fossils in the American West, they also tried their best to ruin each other's professional credibility. Humiliated by his error in reconstructing the plesiosaur Elasmosaurus, Cope tried to cover up his mistake by purchasing every copy he could find of the journal in which it was published. Marsh, meanwhile, made sure to publicize the story. Cope's own rapid and prodigious output of scientific papers meant that Marsh had no difficulty in finding occasional errors with which to lambast Cope. Marsh himself was not infallible; he put the wrong skull on a skeleton of Apatosaurus and declared it a new genus, Brontosaurus.

By the late 1880s, public attention to the fighting between Cope and Marsh faded, drawn to international stories rather than the "Wild West". Thanks to John Wesley Powell, head of the U.S. Geological Survey, and Marsh's contacts with the rich and powerful in Washington, Marsh was placed at the head of the consolidated government survey and was happy to be out of the sensationalist spotlight. Cope was much less well-off, having spent most of his money purchasing The American Naturalist, and had a hard time finding employment thanks to Marsh's allies in higher education and his own temperament. Cope began investing in gold and silver prospects in the West, and braved malarial mosquitos and harsh weather to search for fossils himself. Due to setbacks in mining and a lack of support from the federal government, Cope's financial situation steadily deteriorated, to the point that his fossil collection was his only significant asset. Marsh, meanwhile, alienated even his loyal assistants, including Williston, with his refusal to share his conclusions drawn from their findings, and his continually lax and infrequent payment schedule.

Cope's chance to exploit Marsh's vulnerabilities came in 1884, when Congress began to investigate the proceedings of the consolidated geological survey. Cope had become friends with Henry Fairfield Osborn, then a professor of anatomy at Princeton University. Osborn was like Marsh in many ways, slow and methodical, but would prove a damaging influence on Marsh. Cope searched for disgruntled workers who would speak out against Powell and the Survey. For the moment, Powell and Marsh were able to successfully refute Cope's charges, and his allegations did not reach the mainstream press. Osborn seemed reluctant to step up his campaign against Marsh, so Cope turned to another ally he had mentioned to Osborn—a "newspaper man from New York" named William Hosea Ballou. Despite setbacks in trying to oust Marsh from his presidency of the National Academy of Sciences, Cope received a tremendous financial boost after the University of Pennsylvania offered him a teaching job. Soon after, Cope's chance to strike a critical blow at Marsh appeared.

Over the years, Cope kept an elaborate journal of mistakes and misdeeds that Marsh and Powell had committed; the mistakes and errors of the men were put in writing and stored in the bottom drawer of Cope's desk. Ballou planned the first set of articles, in what would become a series of newspaper debates between Marsh, Powell and Cope. While the scientific community had long known of Marsh and Cope's rivalry, the public became aware of the shameful conduct of the two men when the New York Herald published a story with the headline "Scientists Wage Bitter Warfare." According to author Elizabeth Noble Shor, the scientific community was galvanized:

Most scientists of the day recoiled to find that Cope's feud with Marsh had become front-page news. Those closest to the scientific fields under discussion, geology and vertebrate paleontology, certainly winced, particularly as they found themselves quoted, mentioned, or misspelled. The feud was not news to them, for it had lurked at their scientific meetings for two decades. Most of them had already taken sides.

In the newspaper articles, Cope attacked Marsh for plagiarism and financial mismanagement, and attacked Powell for his geological classification errors and misspending of government-allocated funds. Marsh and Powell were each able to publish their own side of the story, filing their own charges against Cope. Ballou's articles were poorly researched, written, and read, and Cope himself was smarting from a piece in The Philadelphia Inquirer which suggested the University of Pennsylvania trustees would ask Cope to step down unless he provided proof for his charges against Marsh and Powell. Marsh himself kept the Herald story alive with a fiery rebuttal, but by the end of January the story had faded from all the newspapers, and little changed between the bitter rivals.

No congressional hearing was convened to investigate the misallocation of funds by Powell, and neither Cope nor Marsh was held responsible for any of their mistakes, but some of Ballou's charges against Marsh came to be associated with the Survey. Facing anti-Survey sentiment inflamed by western drought and concerns about takeovers of abandoned western homesteads, Powell found himself the subject of larger scrutiny before the House Appropriations Committee. Galvanized to action by Marsh's perceived extravagance with Survey funds, the Appropriations Committee demanded the Survey's budget be itemized. When his appropriation was cut off in 1892, Powell sent a terse telegram to Marsh demanding his resignation, a personal slight as well as a financial one. At the same time, many of Marsh's allies were retiring or had died, lessening his scientific credence. Just as Marsh's extravagant lifestyle was catching up with him, Cope received a position on the Texas Geological Survey. Cope, still reeling from the personal attacks levied at him during the Herald affair, did not take advantage of the change in fortunes to press his personal attacks. Cope's fortunes continued to look up throughout the early 1890s, as he was promoted to Leidy's position as Professor of Zoology and was elected President of the American Association for the Advancement of Science the same year that Marsh stepped down as head of the Academy of Sciences. Towards the latter part of the decade, Cope's fortunes began to sour once more as Marsh regained some of his recognition, earning the Cuvier Medal, the highest paleontological award.

Cope and Marsh's rivalry lasted until Cope's death in 1897, by which time both men were financially ruined. Cope suffered from a debilitating illness in his later years and had to sell part of his fossil collection and rent out one of his houses to make ends meet. Marsh in turn had to mortgage his residence and ask Yale for a salary on which to live. The rivalry between the two remained strong if weary. Cope issued a final challenge before his death. He had his skull donated to science so that his brain could be measured, hoping that his brain would be larger than that of his adversary; at the time, brain size was believed to be a measure of intelligence. Marsh never accepted the challenge, and Cope's skull is reportedly still preserved at the University of Pennsylvania. (Whether the skull stored at the University is Cope's is disputed; the University stated that it believes the real skull was lost in the 1970s, although Robert Bakker has said that hairline fractures on the skull and coroner's reports verify the skull's authenticity.)