In addition to the burden of dealing with the political Presbyterians attacking his college as a devious Anglican plot, and hence leading Presbyterian parents to refuse to send their sons to it, and the usual ramp-up problems of starting a new college, the nine-year-long French and Indian War coincided almost exactly with Johnson's tenure at King's College, drying up funds and draining the pool of potential students while raising fears of invasion. He also had to deal with periodic outbreaks of smallpox, during which he had to leave the college to be run by his tutors for months at a time. Yet he persevered. In the twenty-two year period from 1758 to 1776 when the college closed due to the Revolutionary War, 226 men attended, and 113 graduated. Among the 83 college students who attended King's College during Johnson's -year tenure were some prominent future Loyalists, including Adolph Philipse, Daniel Robart, Abraham De Peyster, and John Vardill. But he taught many more men who became prominent Patriots, including John Jay, Samuel Prevoost, Robert R. Livingston, Richard Harrison, Henry Cruger, Egbert Benson, Edward Antill, Dr. Samuel Bard, John Stevens, Anthony Lispenard, and Henry Rutgers. Among the students taught by his successor Dr. Myles Cooper, were Alexander Hamilton and Gouverneur Morris.