After resigning the presidency of MAC in 1879, Clark left academia to become the president of a mining company, Clark & Bothwell. The company, in operation from 1881 to 1882, purchased several silver mines, mostly in Utah and California. Clark's partner, John R. Bothwell, proved to be corrupt and the company quickly folded, destroying Clark's reputation, his own finances and the fortunes of many of his friends and family. The subsequent scandal ruined Clark's health. He died of heart disease at his home in Amherst in 1886.