The Gardener
Reading Level: Grades 7-10
High school sophomore Mason has a fairly normal life, if you discount the ugly scar marring half of his hulky face; if you discount the disappearance of his father and his mother's drinking habit and tendency to require Mason to be her parent and not vice versa.
When Mason discovers that the Haven of Peace, the rehabilitation center his mom works at is not just for the elderly, but for brain damaged teens whose parents have given up on them in favor of experimentation on them, his life is turned upside down.
After accidentally reviving one of the teens and rescuing her from the Haven of Peace, Mason finds himself on the run from TroDyn, a bioengineering firm responsible for experimentation on the girl.
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Other tales of morally gray experiments on children:
The Maze Runner by James Dashner