In the fall of 1966 he became the newspaper's Pentagon correspondent and in 1968 began reporting on the White House. He was a correspondent on political, diplomatic and military affairs. In 1971 he obtained the Pentagon Papers for the Times. The U.S. government tried to halt publication. The case, New York Times Co. v. United States (403 U.S. 713), saw the Supreme Court reject the government's position, and become a landmark First Amendment decision. The exposé would earn The New York Times a Pulitzer Prize.
In 1970 Sheehan reviewed Conversations With Americans by Mark Lane in the New York Times Book Review (December 27). He called the work a collection of Vietnam War crime stories with some obvious flaws which the author had not verified. Sheehan called for a more thorough and scholarly work to be done on the war crimes being committed in Vietnam.
In November 1974 Sheehan was badly injured in a two-car accident on a snowy mountain road in western Maryland, caused by an uninsured motorist whose driving behavior was arguably criminal in nature. Sheehan's wife, Susan, chronicled details of the accident and its emotional, legal and financial impact in the September 25, 1978 edition of The New Yorker (A Reporter at Large: "The Accident"). In addition to time and effort spent in 1974 fighting three libel suits in connection with a previous book, Sheehan's lengthy recovery from his injuries significantly delayed work on his book, begun in 1972, about John Paul Vann, a dramatic figure among American leaders in the early stages of the war in Vietnam.