Quantico by Greg Bear

From the publisher (source: The Internet Book List):

From the Publisher:
It's the near future - sooner than you might hope - and the war against terrorism is almost lost. Nuclear and biological weapons are in the hands of Islamic radicals, and new weapons are being spawned in remote labs tht can be used against entire populations. These are some of the problems facing three young agents as they finish their training at the FBI Acadamy in Quantico, Virginia.

And still the threat is escalating to ever crazier extremes. The Dome of the Rock has been blown to pieces by terrorists, and in retaliation, thousands have died in another major attack on the United States, the equal of 9-11. Rumours fly through internatonal capitals of a plague targeted to ethnic groups - Jews or Muslims or both. No one feels safe.

Like the Anthrax terror that folowed 9-11, the new plague results from domestic terror, the province of the FBI. The FBI seeks one man who appears to be on a bitter mission to wipe history's slate clean and close the curtain on the modern world.

But the FBI itself is under threat of political extinction. There is a good chance the new agents will be part of the last class at Quantico, 'Cop Valhalla'. As investigations reveal horror upon horror in the US and the rest of the world, the agents join forces with a veteran bioterror expert to foil attacks on the world's greatest religious cities - Jerusalem, Rome, and the Hajj in Mecca.

In the second decade of the War on Terror, victory may be hard to define.

This book is part of the "Quantum Logic" series.
Here are some other books from this series: