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Evil Genius by Catherine Jinks
Cadel Piggott has a genius IQ and a fascination with systems of all kinds. At seven, he was illegally hacking into computers. Now he's fourteen and studying for his World Domination degree, taking classes like embezzlement, forgery, and infiltration at the institute founded by criminal mastermind Dr. Phineas Darkkon. Although Cadel may be advanced beyond his years, at heart he's a lonely kid. When he falls for the mysterious and brilliant Kay-Lee, he begins to question the moral implications of his studies. But is it too late to stop Dr. Darkkon from carrying out his evil plot?
If you like Evil Genius by Catherine Jinks you'll want to check out the other books in the series:
Genius Squad and The Genius Wars
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The Cabinet of Wonders by Marie Rutkoski
This is the tale of twelve year old Petra. She travels to Prague with her magical tin spider hoping to retrieve the enchanted eyes the Prince of Bohemia took from her father. She meets a Roma boy and his sister who help her in her quest.
H.I.V.E.: Higher Institute of Villainous Education by Mark Walden
Swept away to a hidden academy for training budding evil geniuses, Otto, a brilliant orphan, Wing, a sensitive warrior, Laura, a shy computer specialist and Shelby, an infamous jewel thief, plot to beat the odds and escape the prison known as H.I.V.E.
The Mysterious Benedict Society by Trent Lee Stewart
This is the story of four kids who pass a series of mind-bending tests and are selected for a secret mission that requires them to go undercover at the Learning Institute for the Very Enlightened. The only rule is that there are no rules.