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 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." 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.
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.