Rogue

Description for ROGUE by Mark Walden:

The leaders of the world's villainous forces are being picked off one by one in a series of mysterious attacks, and when Dr. Nero finds out it is Otto who's behind them, he has no choice but to issue a "capture or kill" order. Raven and Wing are desperate to save their friend and soon find themselves in a danger-filled race against time to track Otto down before other assassins get to him. Their pursuit takes them to a secret facility hidden deep within the Amazon rain forest, where they face a deadly mysterious operative.

Meanwhile, back at the Higher Institute of Villainous Education, the school's own automated defense systems turn against the pupils and staff of H.I.V.E. -- and there is no one there to stop them....

This is #5 in H. I. V. E. Series.