Much like biblical texts such as the epistles that address very specific issues relevant to Christians of different eras, the novel Thr3e by Ted Dekker explores themes and ideas that Christians in modernity frequently struggle with. Dekker uses a more figurative format than he does in his other works (which typically deal directly with the supernatural, including angels and demons, or alternate realities engaged in spiritual warfare), choosing instead to create a metaphor for repentance and salvation through the eyes of a man marked for death.

Thr3e addresses what the author sees as a prevalent trend of moralism and liberalism in the church and in biblical interpretation that tends to teach that being "good enough" will enable Christians to attain salvation. Dekker puts forth the opposing idea that, according to the Bible, the only way to truly attain salvation is through confessing and repenting of one's sins and accepting Jesus's sacrifice on one's behalf. The protagonist of the novel, Kevin Parson, represents Christians who believe that if they are morally good, they will be accepted by God.

Dekker's emphasis in the novel is on the idea of repentance: the killer, Slater, refuses to allow a pardon on behalf of the good works or even biblical knowledge of the protagonist (who is well versed in scripture, having studied for several years at a seminary to enter Christian ministry). The only way for Kevin to save his life is to confess his sins. Dekker is making a very deliberate point that, in his view, there is no salvation except through repentance and confession.

He also stresses the idea that death is an ever-present issue for humanity. In spite of Kevin's seminary education, the ideas of death and salvation are far from his mind at the beginning of the novel. Dekker suggests that in a modern world where many people's basic needs are taken care of, and that care is taken for granted, it is easy to overlook the reality of death. His aim is to use this novel to bring the inevitability of death to the forefront of believers' minds so that they will acknowledge their sin and repent of it.