Together with Bernard Trainor, he has written two books: The Generals' War: The Inside Story of the Conflict in the Gulf, which covers the 1991 Gulf War, and Cobra II, which covers the Iraq War begun 2003.

The General's War won high praise from several critics and decisionmakers, with then Defense Secretary Dick Cheney describing it as "a fascinating account of the war" that he would "recommend" "as something that gives them a different element of some of the key decisions that were made." Jim Lehrer described it as "A superb account and analysis of what went right and what went wrong in the Gulf War"; and Eliot Cohen, writing in Foreign Affairs, called it "the best single volume on the Gulf War."

Cobra II, which "focuses on the rushed and haphazard preparations for war and the appalling relations between the major players," won praise from Lawrence Freedman in Foreign Affairs, who wrote that "the research is meticulous and properly sourced, the narrative authoritative, the human aspects of conflict never forgotten." Gordon's paper, the New York Times, called it "a work of prodigious research", adding that it "will likely become the benchmark by which other histories of the Iraq invasion are measured." The New Republic, while calling the book "splendid", wrote that "Gordon and Trainor remain imprisoned in an almost exclusively military analysis of what went wrong...(which)..unintentionally underplays the essential problem in Iraq--the problem of politics."

From West Germany on New Years Day in 1989, Gordon, together with Steven Engelberg broke the news that Imhausen-Chemie, a West German chemical company, had been serving as the "prime contractor" for an alleged Libyan chemical weapons production plant at Rabta since April 1980. The article was based a leak to Gordon "by U.S. administration officials of data that the United States previously had asked West Germany to keep secret". The German government initially denied the allegations, but following further reports on the Rabta plants and pressure from the US administration, a total of three Imhausen employees, including the director, were convicted of illegally supplying CW materials to Libya in October 1991 and a fourth German national was convicted in 1996 for "facilitating Libya's acquisition of computer technology and other equipment to enhance chemical weapons development".

Gordon and Engelberg won a George Polk Award for international reporting following their series of articles.