Bodeen, S.A. The Gardener.
Life is not easy for Mason. He was attacked by a dog and disfigured at an early age, his father is not in the picture, and his mother works very hard at a local nursing home but unfortunately copes with her distress by drinking. She is adamantly opposed to TroDyn, a local scientific corporation that runs much of the town but represents Mason's best chances at college. Things take an even stranger turn when Mason visits the nursing home at which his mother works and meets a catatonic young girl who is awakened by a videotape of Mason's father reading Margaret Wise Brown's The Runaway Bunny. Laila is desperate to escape the nursing home but freaked out by anything that has to do with TroDyn-- for good reason. Without spoiling the suspense, suffice it to say that TroDyn is pursuing an ultimate good by means of a horrible evil, and Mason's entire existence is tightly wrapped up in the fortunes of the company.
Like Bodeen's The Compound, (which has been HUGELY popular in my library) this is an innovative and compelling science fiction thriller with a dash of mystery. The reviews for this book do not treat the writing kindly, but I didn't have a problem with it. Surly Teen Boy didn't like the ending, and I quite honestly forgot it after a day, so perhaps the writing could have been stronger, but for students who need or want science fiction, I think this will be a popular choice. It could also be tied in to a science unit on autotrophic organisms.
And if you want to make a children's librarian creeped out, quoting The Runaway Bunny in such an evil context is a good way to do it!