Bones of Empire — William C. Dietz

In a far-distant future, the Uman Empire has conquered and colonized worlds. Once thought invincible, its reign is now fragile as alien subjects and enemies conspire against it....

Jak Cato is a cop -- bioengineered to see through the guises of the vicious shape-shifting aliens known as the Sagathies. Once a guard on the prison planet where they are confined, he risked his life hunting down a Sagathi who escaped.

Now Cato is on assignment in the capital city of the Uman Empire. One day he gets a glimpse of the Emperor -- and realizes that what he is looking at is not human. It is the supposedly dead shifter.

With only a few allies to assist him, Cato must determine if the alien is acting alone to bring down the hated Umans or if he is part of some even larger conspiracy. Cato knows only two things: The fate of the Empire, and his own honor, is at stake....

And his mortal enemy is still alive and once again on the run.