Spider Games by Brian Falkner

Nick is a little different - nervous, timid and socially awkward, absolutely the wrong person to be caught in a deadly spy game of cat and mouse. But when his grandfather vanishes during a trip to Berlin and long-buried secrets begin to surface, Nick finds himself alone with sinister figures closing in. His only ally is Rejhana who is carrying dangerous secrets of her own. Survival becomes a matter of trust, and what makes him different could be the key to everything. As the world counts down to the new millennium, Nick and Rejhana are out of options, out of luck and out of time in the city of spies.