The story I read is called Artemis Fowl, the Eternity Code. This wonderful book was written by Eoin Colfer.

The novel starts out as Artemis, a thirteen-year-old boy genius tells about his father, coming back from his kidnap by the Russian Mafia. Artemis has created a supercomputer with the remains of stolen Lower Elements Police technology that will render all present day technology obsolete. He plans to meet with the powerful CEO of Fission Chips, John Spiro. But Spiro springs a trap, stealing the C-Cube and mortally injuring Butler, Artemis's only companion. Artemis knows the only way to save his loyal bodyguard is to employ fairy magic; so once again, he must contact his adversary-turned friend, Captain Holly Short of the LEP. And once again, Holly heals Butler, but to have him age about fifteen years. Holly is on an important mission, and has to leave right away...