While pursuing his master's degree in counseling from the University of Oregon, Griffin attended a lecture series delivered by Paul Tillich at the Graduate Theological Union in Berkeley, California.

Following the September 11 attacks, David Ray Griffin shifted his focus from questions of philosophy and religion to ones of politics and history, specifically American expansionism and imperialism.

He intended to write a book on the subject, presenting 9/11 in terms of "blowback" for aggressive United States foreign policies of the 20th century: Until the spring of 2003, I had not looked at any of the evidence.

[11]After reading the work of Paul Thompson[12] and Nafeez Mosaddeq Ahmed,[13] he became convinced that there was a prima facie case for the contention that there must have been complicity from individuals within the United States government.

[5] Part One of the book looks at the events of 9/11, discussing each flight in turn and also the behaviour of President George W. Bush and his Secret Service protection.

David Ray Griffin discussed this book and the claims within it in an interview with Nick Welsh, reported under the headline Thinking Unthinkable Thoughts: Theologian Charges White House Complicity in 9/11 Attack.

"[24][25] In 2006, Griffin, along with Peter Dale Scott, edited 9/11 and the American Empire: Intellectuals Speak Out, a collection of essays including Steven Jones' paper Why Indeed Did The World Trade Center Towers Collapse?.

[30] At the end of one of his lectures entitled 9/11: The Myth and the Reality Griffin was asked why a theologian would be one of the primary speakers for the cause (of questioning the official version of events), and was asked to explain whether he saw any religious or spiritual implications of 9/11, to which he replied: "If the religions of the world are correct ... the Divine cares about ... the long-term good of the world ... And wouldn't want ... nuclear wars that would decimate all life on the planet, wouldn't want global warming to continue ... so I'm convinced that this administration ... is the most dangerous administration we've ever had for the future of this country and the future of the world, and if trying to save god's planet is not a religious issue, I wouldn't know what was.

[32]David Aaronovitch, in the London Times in 2008, wrote: "Griffin believes that no plane hit the Pentagon (despite hundreds of people seeing it) and that the World Trade Centre was brought down by a controlled demolition.

[35] Griffin attempts to resolve this problem in two ways, first by providing an exhaustive critique of contemporary discussions of the problem (e.g.,Thomas Nagel, John Searle, Galen Strawsen, Colin McGinn, Geoffrey Madell, Karl Popper, Jaegwon Kim, and Owen Flanagan[36][37]) and then providing an “alternative for 'fully naturalizing’ the mind' based upon the process metaphysics of Alfred North Whitehead and Charles Hartshorne.”[38] Griffin's alternative rejects the metaphysical assumption shared by dualism and materialism that matter is insentient[38][37] arguing that this shared assumption about matter leads to apparently unresolvable problems such as how experience arose out of non-experiencing natural entities[38][39] or how conscious experience can be described in physicalist terms.

"[47] Despite their philosophical importance to Griffin, however, he believes that the "precise formulations of hard-core ideas are always fallible"[47] and so must "function not as a foundation upon which all other beliefs are to be built but as a compass telling us when we have gotten off course.

[51][52] For example, Paul R. Gross, Norman Levitt, and Martin W. Lewis assert that, "The overwhelming majority of scientists consider parapsychology, by whatever name, to be pseudoscience.

"[53]  Griffin proposed that the explanation for this majority opinion lies in a shared late modern worldview, which assumes materialism and rejects action at a distance, rather than from fair and impartial examination of the evidence.

[37][54] According to Griffin, "Intellectuals who share this ... materialistic worldview more typically reject the evidence [for paranormal phenomenon] out of hand, either by refusing to examine it or by attacking the credibility of those reporting it ...".

[56][57] Griffin states that the evidence from parapsychology as well as the persistent belief in these other values have led to a "growing realization that [the] late modern worldview is ... inadequate intellectually.

"[58] His judgement was that people should move to a postmodern worldview that can consistently and coherently recognize the possibility of paranormal events as well as the reality of intellectual, moral, and esthetic norms.