Clover Omnibus (2009)

Kazuhiko is a young, but already deeply wounded black ops agent of a baroque, retro-tech future — pulled out of retirement to escort Sue, a mysterious waif, to a destination she alone knows. Sue and Kazuhiko have never met, yet she knows him, having grown up since the age of four with her only human contact, two distant voices: that of her elderly "grandma," General Ko, and of Kazuhiko's dead girlfriend, Ora. And Sue has been kept in that cage all these years because of what she is, and what the Clover Leaf Project found her to be — a military top secret, and the most dangerous person in the world!