Wildlife Depletion
At the forefront of the story thematically-speaking is wildlife depletion and the increasing rate of extinction. The story of the human protagonist, Kester Jaynes, plays out against a background in which a plague has caused widespread and mass extinction of animals around the globe. And as if that weren't bad enough, the government is aiming to finish the job that nature has left incomplete. In a post-narrative section of the book, the author asserts that he was urged to write the book precisely because of the profound emotions he felt at the rate of extinction of wildlife.
Critique of Capitalism
The government policy to finish what nature started is inextricably tied to its relationship with a conglomerate called Facto which produces food it claims is necessary to maintain human life while the plague devastates animals and crops. Amazingly enough, however, it turns out that Facto has been lying. In fact, they have not only been lying about their good intentions to cover up their true aim to make the entire population dependent upon their food, but they have also invented myths about the nature of the plague itself. All with the express cooperation of the government, of course.
Bullying
The young protagonist, Kester, faces harsh bullying at Spectrum Hall, a home for "troubled" kids. It is not just the other boys who bully him, but the adults as well. A doctor is particularly cruel. The bullying of Kester is juxtaposed against the treatment of the animals that survived the plague as well as Facto's handling of its business model. The result suggests very strongly that bullying is not limited to jerky schoolkids by any means.
