Character Description
Keep in mind this is a book written for a target audience not yet even in high school. As a result, similes are plentiful. Plentiful because they are effective shorthand for conveying information and plentiful because the narrator is a kid and kids use the comparative qualities of similes a lot:
"Whoever is speaking has a very deep voice—it's not a kid's voice at all, or even a man's—it rasps and echoes, like a rock rattling down a metal pipe."
The Plague
The backstory here is the onset of a plague which causes mass extinction of animals and crops. It is referred to as the "red-eye" in familiar terms rather than the plague. Metaphor helps to explain why:
"A flu that turned animal bodies and brains to mush and, just before they died, made their eyes burn bright red like they were on fire inside."
Spectrum Hall
The narrator/protagonist is a student at Spectrum Hall. Or, more specifically: Spectrum Hall Academy for Challenging Children. One of the first uses of similes is directed toward describing the building housing this academy:
"The corridor with the cameras and the fat warden is on the seventh floor of a building which like a big upside-down boat made of glass and metal."
Captain Skuldiss
Captain Skuldiss is not a nice man. If there was any doubt about this fact, it should be extinguished when he brags to children about having killed before and, what's more, how the first time is always the hardest. And then there are his eyes:
"His eyes stare up at me, as calm and murky as two stagnant ponds."
Darkness
The defining metaphor of the modern age can be counted on to appear even in the most optimistic of novels. Any thought that it would not show up in a dystopian futuristic tale can be immediately cast aside:
"I want to clap my hands and clear the craziness from my head. My brain crackles once more and my eyes grow heavy, as my thoughts slide back down into the darkness."
