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The End of Faith Portrays an eyeglass view of the final day in the life of a suicide bomber. Harris calls for an end to respect and tolerance of the belief systems of mainstream religion. He accuses religious people of "having beliefs for which there is no rational justification," adhering to paradigms that are "all equally uncontaminated by evidence." Religious fundementalism is prevalent because of the very moderates who are at fault for their toleration of the vitriol spouted by the fundementalists.

His examinination of the nature of belief itself, leads to a conclusion that freedom of belief presents a hazard. Any belief must be logical, coherent, and truly represent reality. But religious belief fails to rely on empirical evidence. Harris likens religion to mental illness which denies reality.

Harris follows this with a brief survey of Christianity down the ages, examining the Inquisition and persecutions of witches and Jews. He contends that, far from being an aberration, the torture of heretics was a logical expression of Christian doctrine – one which, he says, was clearly justified by men such as Saint Augustine. Going still further, Harris sees the Holocaust as essentially drawing its inspiration from historical Christian anti-Semitism. "Knowingly or not," he says, "the Nazis were agents of religion."

Among the controversial aspects of The End of Faith is an uncompromising assessment and criticism of Islamism, which Harris describes as being a "cult of death." He infers a clear link between Islamic teaching and terrorist atrocities such as 9/11, a notion he supports with quotations from the Koran that call for the use of violence.

He also presents data from the Pew Research Center, purporting to show that significant percentages of Muslims worldwide would justify suicide bombing as a legitimate tactic.[1][2] In an attack on what he terms "leftist unreason," Harris criticises Noam Chomsky among others for, in his view, displaying an illogical willingness to lay the entire blame for such attitudes upon U.S. foreign policy.

However, Harris also critiques the role of the Christian right in the United States, in influencing such areas as drug policies, embryonic stem cell research, and AIDS prevention in the developing world. In what he sees as a steady drift towards theocracy, Harris strongly criticises leading figures from both the legislature and the judiciary for what he perceives as an unabashed failure to separate church and state in their various domains. "Not only do we still eat the offal of the ancient world," he asserts, "we are positively smug about it."

Next, Harris goes on to outline what he terms a "science of good and evil" – a rational approach to ethics, which he claims must necessarily be predicated upon questions of human happiness and suffering. He talks about the need to sustain "moral communities," a venture in which he feels that the separate religious moral identities of the "saved" and the "damned" can play no part. But Harris is critical of the stance of moral relativism, and also of what he calls "the false choice of pacifism." In another controversial passage, he compares the ethical questions raised by collateral damage and judicial torture during war. He concludes that collateral damage is more ethically troublesome. "If we are unwilling to torture, we should be unwilling to wage modern war," Harris concludes.

Finally, Harris turns to spirituality, where he especially takes his inspiration from the practices of Eastern religion. He writes that there have been mystics in the west and calls some of these "extraordinary men and women", such as Meister Eckhart, Saint John of the Cross, Saint Teresa of Avila, Saint Seraphim of Sarov, but that, as far as Western spirituality is concerned, "we appear to have been standing on the shoulders of dwarfs." He discusses the nature of consciousness, and how our sense of "self" can be made to vanish by employing the techniques of meditation. Harris quotes from Eastern mystics such as Padmasambhava and Nisargadatta Maharaj, but he does not admit any supernatural element into his argument – "mysticism is a rational enterprise," he contends, "religion is not." He later elaborates: "The mystic has reasons for what he believes, and these reasons are empirical." He states that it is possible for one's experience of the world to be "radically transformed", but that we must speak about the possibility in "rational terms".