Tsubasa: those with wings

Tsubasa Those with Wings is a trilogy by Natsuki Takaya, author of Fruits Basket (Furuba) and Songs that Make You Smile- a collection of shorts.

Set in the 22nd century, where all the world has been broken up into three major countries, ex thief Kotobuki and her ex-army friend Raimon go on a long adventure, risking their life and falling in love ♥? With help from Shoka, Kotobuki's ditzy thief friend, Shoka's lackeys, and Adelaide, a brilliant business girl, and rich friend,and Yan, the young leader of a  they trace Tsubasa, a mysterious artificial pair of human brains, that have the ability to grant wishes, all the way to now-mythical Japan.

Kotobuki  is the only one to see Tsubasa in action, until she begs it to forgive her and the rest of human kind; However, she has one main goal, to free Raimon from his army superiors, who exert some sort odd control over him.