This is a fanfic for a (sadly) not well known series called Phantom: Requiem for the Phantom. It's my favorite anime and I love it to death (though the time skips are a bit unrealistic, especially the last one before the ending. there is no way Cal could age that much in two years!!!)

*SPOILERS AHEAD!!!*

 The series is about two assassins named Ein and Zwei (one and two in German) who are forced to work together for a crime syndicate called Inferno as the infamous assasin Phantom.

info: http://en.wikipedia.org/wiki/Phantom_of_Inferno#Anime_series

episodes: http://en.wikipedia.org/wiki/List_of_Phantom:_Requiem_for_the_Phantom_episodes

As the series progresses we meet a young girl named Cal. After a bomb goes off in their apartment Reiji (they were living together because the woman Cal was living with was murdered by a rouge assassin. It's not weird, she's ten.) believes Cal is dead, and having found Ein, must leave the country immediately. Cal knows Reiji thinks she's dead, but luckily she was out shopping when the bomb went off.

 When she sees the bomb go off on her way home, she runs to the apartment calling desperately for Reiji. After Reiji doesn't answer her, Cal feels betrayed. Scythe Master appears saying Reiji tricked her and twists her sadness to pure anger. She leaves the wreckage of the apartment with Scythe Master.

 After this there's a two year lapse during in which Inferno works with Scythe again after thinking they were tricked by Claudia, and Cal becomes the third Phantom, Drei.

 This fanfic takes place from Cal's point of view during those two years.