In terms of poetry, he is best known for his book-length poem Coming to Jakarta (subtitled "a poem about terror"), which describes in measured, prosodically regular verse the 1965 crisis in Indonesia that resulted in the Indonesian Civil War and the deaths of as many as half a million people, in which he believed the CIA to play a role.

Scott is far from a stridently political poet, working always to connect the polemical to the personal. In Coming to Jakarta he writes:

To have learnt from terror        to see oneself    as part of the enemy

can be a reassurance

In the context of this emotional and psychological side of conflict, Scott alternates between descriptions of his own life..."dressed up in polished / gaiters with a buttonhook"...and the massive violence of his principal subject. Somewhere between confessional and scholarly, his poems often contain citations in the margins.

Scott has described his poem Minding the Darkness as his most important, though he concedes that "Like other long poems by older men. . . it toys dangerously with abstract didactic principles."Introductory matter to excerpts from Minding the Darkness, . The poem is intended as the culmination of a major poetic project of which Coming to Jakarta was the inception.

Scott has researched and written several investigative books about the role of the "deep state" (as opposed to the "public state"). However, Scott rejects the label of "conspiracy theory" and has used the phrase "deep politics" to describe his heavily-footnoted political writing. The investigative bent has spilled over into his works of poetry, some of which must contain marginal notes to explain to readers which documents or real-world news events are being referred to. His most recent book, The Road to 9/11 from the University of California Press, deals with historical and geopolitical context of the events of 9/11, and describes "how U.S. foreign policy since the 1960s has led to partial or total cover-ups of past domestic criminal acts, including, perhaps, the catastrophe of 9/11."

An interesting aspect of Scott's work that combines both his investigating interests and his poetry is illustrated by The Global Drug Meta-Group: Drugs, Managed Violence, and the Russian 9/11The Global Drug Meta-Group: Drugs, Managed Violence, and the Russian 9/11, .

Political

• The War Conspiracy (1972, out of print)
• The Assassinations: Dallas and Beyond (in collaboration, 1976, ISBN 0-394-40107-7)
• Crime and Cover-Up: The CIA, the Mafia, and the Dallas-Watergate Connection (1977, ISBN 0-87867-066-1)
• The Iran-Contra Connection (in collaboration, 1987, ISBN 0-89608-291-1)
• Cocaine Politics: Drugs, Armies, and the CIA in Central America (in collaboration, 1991, 1998, ISBN 0-520-21449-8)
• Deep Politics and the Death of JFK (1993, 1996, ISBN 0-520-20519-7)
• Deep Politics Two: Essays on Oswald, Mexico, and Cuba (1995, 2007, ISBN 0-9790-0994-4)
• Drugs Oil and War (2003, ISBN 0-7425-2522-8)
• The Road to 9/11: Wealth, Empire and the Future of America (September 2007, ISBN 0-5202-3773-0)
• The War Conspiracy: JFK, 911, and the Deep Politics of War (2008 reissue and expansion of 1972 edition) (July 2008, ISBN 978-0980121360)
• American War Machine: Deep Politics, the CIA Global Drug Connection, and the Road to Afghanistan (November 2010 - ISBN 978-0742555945)

Poetry

• Coming to Jakarta: A Poem About Terror (1989, ISBN 0-8112-1095-2)
• Listening to the Candle: A Poem on Impulse (1992, ISBN 0-8112-1214-9)
• Crossing Borders: Selected Shorter Poems (1994, ISBN 0-8112-1284-X)
• Minding the Darkness: A Poem for the Year 2000 (2000, ISBN 0-8112-1454-0)
• Mosaic Orpheus (2009, ISBN 978-0-7735-3506-0)