The themes of Encrypted are probably best summarized in the Four Core Principles enunciated and promoted by the Collective.  These are:

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• Pleasure—the purpose of life was the attainment of pleasure

• Permanence—pleasure once attained must be preserved as long as possible—life was to be extended indefinitely 

• Transparency—knowledge, as a source of pleasure, must be universally available—all knowledge belongs to all sen-kind

• Entitlement—the Collective exists to provide the individual with the means to attain the first three principles

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Of course, as you might surmise of any philosophy promoted by the Collective, the Core Principles are a siren's song, seductive but leading to personal destruction.

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Let's take them one at a time.

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The Pleasure Principle:    By its very nature, pleasure is an inward looking perspective--the good and bad of everything is evaluated and determined by how it affects me.  It is the ultimate "me-centric" philosophy.  As such, it partakes of the original sin--pride or what the Greeks called "hubris".  It makes the individual his own god.  Indeed, pleasure, focused on satisfying the desires of the individual, encompasses all of the original seven deadly sins--pride, lust, avarice, sloth, gluttony, envy and wrath.  There is no objective truth; neither good nor evil except as it adversely or beneficially affects the individual.  

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The Permanence Principle:    The Collective promotes the immortality of the flesh--that physical life was to be extended indefinitely.  Christianity also believes in eternal life--but not the immortality of the flesh, rather the immortality of the spirit.  The Christian view is that the physical life is transitory; it is a stage of development that is intended to lead  to a more perfect and eternal life of the spirit in harmony with God.  The result of the indefinite prolongation of the physical life is that man's spiritual development is arrested and the path to Heaven is blocked.

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The Transparency Principle:    This is the one Core Principle that is good in the abstract, but which has been perverted by the Collective in practice both as to its objective and application.  The Collective views transparancy as a means to promote knowledge which it sees as a source of pleasure.  Thus, as Citizen Lucy argues, when transparency reveals knowledge that the Collective views as "inimical to the common good," it must be suppressed.  In the Collective's view, the principle is to be selectively, not universally, applied.  In his inquisition dialogue with Citizen Lucy, Thomas disputes this.  He argues that the true goal of Transparency is the promotion of objective Truth and knowledge of the Truth is essential because it enables the  individual's freedom to choose.  Thus, the proper goal of transparency is the promotion of freedom.  To Lucy, this is "apostasy"--"freedom means inequality; super-abundance for the few and want for the many."  To Citizen Lucy, "[f]reedom was always an over-rated commodity--bargained away by the masses for ease and entitlement."

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The Entitlement Principle:    Entitlement is the "raison d'être" of the Collective--the Collective exists to attain for the individual the first Three Core Principles.  The pursuit of pleasure has replaced the quest for the Truth; the selective application of transparency denies the individual access to the Truth and subverts his/her freedom to choose.  The Book must be suppressed because its competing Truth promotes the freedom of the individual to choose between good and evil.  The central event of the Old Testament was the story of Moses leading the Israelites out of slavery in Egypt to freedom in the Promised Land.  The New Testament sounds a similar theme when Jesus replaces the complex web of laws enshrined in the Old Testament with two simple commandments based on love--love God and love your neighbor.   Freedom is essential because it provides the means for attaining the good--an individual achieves the good by freely choosing Truth over Falsehood, Good instead of Evil, Love instead of Hate, Righteousness instead of Sin.  Entitlement enslaves sen-kind by subverting freedom.