The motif of threat and terror
There is a constant threat against Alleg's well-being throughout the book. They threaten him and his family. They make him wonder if they are torturing his wife next door, and they torture him with absolute pain, so that their threats are heeded. When he denies them information, they threaten to kill him, to show him new kinds of torture, to starve him, to harm his loved ones—it is an exhaustive attempt to use threat and terrorism to control him.
Depictions of bodily torture
There is a motif of torture devices, showing the various types of strategies they employed to convince him to betray his homelands. They waterboard him, a form of torture he was previously unfamiliar with. He genuinely believed they were going to slowly drown him to death, and of course, they probably would have. The depictions of torture are physical, literal symbols of human evil and hatred.
Torture as injustice
Torture is shown to be a violation of Alleg's divine sovereignty. They treat him as if his life has no inherent worth, which is the hallmark of injustice. By tying him down and torturing him, they disenfranchise his human right to existence itself, by making him fear death certainly, but also by delivering so much pain and torture to his human body that he craves a death that will not come. He wants to survive, but his experience of reality is permanently changed by horrendous experiences of pain.
The motif of martyrdom
By not speaking, Alleg becomes a witness to the true brutality of military torture. They view themselves as gods who lord their freedom over Alleg by treating him with pure malice. They make him a martyr of the human experience, because he has to witness true evil done in the clandestine protection of government agencies. By writing the book, he finally speaks, but not about military intelligence—he speaks about human nature and the problem of torture.
The symbolic use of chemicals
By using chemicals that change Alleg's ability to perceive reality, the symbolic lines of autonomy are finally crossed in literal truth. Although they had being using torture to persuade Alleg to betray his community by helping them with military intelligence, the use of Pentothol is an outright demonstration of their intent. They don't care about his soul or life whatsoever—they just want to extract intelligence from his brain.