The Shadow Cabinet by Maureen Johnson

In her weakest moment, Rory will find true strength
Grieving, shaken, and feeling very much alone, Rory's life as a member of the Shades of London has changed irrevocably. It's only been a matter of hours since Stephen was taken from her, possibly for ever. Her classmate Charlotte is still missing, kidnapped by the same people who tried to take Rory. Rory is no longer a schoolgirl haplessly involved in the dealings of a secret government unit. She is their weapon in a matter of life and death.
With hardly a moment to think for herself, Rory gets back to work. Charlotte must be found - as must Stephen, if he is even out there. Lines must be drawn and forces rallied. Something is brewing under London, something bigger and much more dangerous than what has come before. The Shadow Cabinet holds the key to everything, and it is up to Rory to unravel its mysteries before time runs out...