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 have played 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." The poem is intended as the culmination of a major poetic project of which Coming to Jakarta was the inception.
Scott has written about the role of the "deep state" (as opposed to the "public state"). Rejecting the label of "conspiracy theory", he has used the phrase "deep politics" to describe his political concerns. His interest in contemporary history 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 book, The Road to 9/11 (2007), deals with geopolitical context of events leading to 9/11, and argues "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." His books The Road to 9/11 and American War Machine are available in French under the titles La Route vers le Nouveau Désordre Mondial and La Machine de Guerre Américaine. The latter was reviewed in March 2011 by Bernard Norlain, a retired French five-starGeneral of the Air Force. In all, his books have been translated into French, German, Italian, Spanish, Russian, and Bahasa Indonesia. His articles have been translated into 16 languages, including Turkish, Arabic, Farsi, Chinese, and Japanese.
Of Scott's book, American War Machine: Deep Politics, the CIA Global Drug Connection, and the Road to Afghanistan (2010) Daniel Ellsberg commented: "I said of Scott's last brilliant take on this subject, Drugs, Oil and War, that 'It makes most academic and journalistic explanations of our past and current interventions read like government propaganda written for children.' Now Scott has written an even better book [...]"
An 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 9/11.
Scott's Deep Politics and the Death of JFK was published in 1993 University of California Press.Kirkus Reviews called the book a "[s]taggeringly well-researched and intelligent overview not only of the JFK assassination but also of the rise of forces undermining American democracy". The Kirkus review also described as a "kind of Rosetta stone for cracking open the deepest darkness in American politics."Publishers Weekly said that Scott's "thoughtful, extremely (and sometimes excessively) detailed book promises more than it actually delivers" and that "the 'facts' on which he relies are often the result of other people's not necessarily accurate reporting". According to PW, "[t]he book's most useful feature is a careful discussion of how U.S. Vietnam policy changed abruptly after Kennedy's death."
Professor Emeritus of Criminology at Pennsylvania State University, Alan A. Block, described 'Deep Politics' as "A masterful synthesis of decades of research into President Kennedy's assassination. Weaving together the malevolent common interests... most likely responsible for the assassination," adding that, "Scott's work is a major contribution to assassination research and, indeed, the social history of modern America. This work sets the standard for all future inquiries into the assassination." 
Gaeton Fonzi, an investigative journalist hired as a researcher via the Church Committee and House of Representatives Select Committee on Assassinations in 1975 and 1977 respectfully, stated that "No one provides a broader and more revealing perspective. From what he calls 'the underlying continuities of deep politics' to the mutual interests of military, right-wing, intelligence agency and organized crime conspirators, Scott's selective revelations move the Kennedy assassination into the historical context all Americans must first grasp before they can truly understand the consequences that terrible event had—and still has—on their lives."
In a 2004 review for The Wilson Quarterly, Max Holland wrote that "Deep Politics is an unreadable compendium of 'may haves' and 'might haves,' non-sequiturs, and McCarthy-style innuendo, with enough documentation to satisfy any paranoid." Shortly thereafter, Holland reiterated similar comments in a second piece written for Reviews in American History and criticized the University of California Press' editorial committee for approving the publication of the book: "This peer approval by a major university press illustrates the boundless and utter disbelief in the Warren Report that exists even in the highest reaches of the academy, and it also reveals the gross inattention given to the subject by serious historians." Scott responded with a letter to the editor stating: "I was disappointed to see those who have published me attacked vigorously for doing so by a major historical journal. I continue to believe that it is the job of the academy to open minds, not to close them." Furthermore, Scott argued that it was "gross intellectual cowardice to allege or imply falsehoods without supporting this accusation", and that "One might have thought in a 19-page attack... there would be at least a paragraph dealing with what I had actually written." Adding that, "Holland demonstrates at the outset that he has done no basic research on Oswald, whom he believes to be the only important person in the case." 
In 2013, the founder of Salon news website, David Talbot, included 'Deep Politics and the Death of JFK' in his list of top seven "best books on the subject", describing the work as a "masterpiece, a meticulously detailed examination of the deep network of power that underlies the events in Dallas.... filled with provocative insights about how the upper circles of U.S. power actually operate."