Train, better known as Black Cat, completes another mission for Chronos, and is informed of his next mission. Later, Sven is inside a restaurant, planning how to catch his next target. A parade is happening outside, celebrating a new governor coming into office. One of the waitresses informs Sven that the new governor is also a gangster, the same man that Sven is targeting. A party is held that night, and Sven learns he isn't the only one targeting the governor. The infamous Black Cat is as well, though with a very different objective...

Sven goes back to his usual sweeper to find some more work. Not long after, a girl runs in with a couple of thugs not far behind. Sven steps in and drives the thugs off. After talking to the girl, he finds out that the thugs have her little sister hostage, and she has the ransom money for her sister's return. She offers Sven the money if he can get her sister back. Will Sven take the job?

Coming back from his first failed attempt to bring back Train, Creed returns. With Train fully turning his back on Chronos it is all up to Creed. Since his first attempts failed Creed uses his magic to kidnap Train. When that doesn't work he goes for the thing Train cares about the most... Saya. Can Train stop him?

Train awakens in Sven and Eve's company. Confused and saddened, he has to decide what course of action to take with his life next. As Sven goes out to get supplies, Eve comes to realize that she has to repent for her sins as well. Meanwhile, someone from Chronos is close by, looking to capture Eve.

Rinslet Walker accepts a dangerous new job, seeking help, she looks for Sven to ask for his assistance. Meanwhile, coming to a new town, Sven, Eve and Train look for their next target, a man who works at the town's garden. Unbeknown to them, a group known as the Apostles of the Stars, people bent on the destruction of the world, are also targeting this man, though for a different reason.

A summit conference between leaders is being held, and the Apostles of the Stars plan to interrupt it in the form of a revolution. Train, learning that Creed is alive, goes to confront him, abandoning his friends in the process. Eve and the others follow to try and stop the Apostles of the Stars from causing chaos. Sven has a terrible vision, and races to find and protect Train from powers beyond his current state.

A man named Woodney, claiming to be the legendary assassin, Black Cat, meets Eve. Eve helps him out of a potentially dangerous situation. Soon afterwards, a member of the Apostles of the Stars, Durham, appears, eager to kill Black Cat. Train saves Eve and Woodney, and then confronts the gunman. Who is the superior gunman, Train or Durham?

Sven learns of a group of sweepers that gather and team up to take out the more dangerous targets. After discovering that the group is after Creed Diskenth, Sven tries to prevent Train from learning, worried that this will cause Train to recklessly go after Creed again. To distract him, Sven has Train and Eve help a woman get back her pet lizard, Flora. They soon find out that this isn't the easy task they expected, as Flora isn't an ordinary lizard.

Train travels toward a port where he can get a boat to reach Kraken Island, where the Apostles of the Stars are. He decides to take a faster route, and goes through a dangerous canyon. Train soon collapses, and later awakens in a strange house. He meets a girl who looks remarkably like Saya. He stays there for a while, and learns more about this mysterious girl called Saki, and of the troubles that confront her.

Having returned from their mission, Train and the others rejoice. Rinslet discovers something called The Eden Project, meanwhile, members of Chronos betray the organization. Sven decides that Eve should leave, and go on to live her own life with girls her own age. Eve however, doesn't want to leave him, and runs off to think for a while. Unbeknownst to the group, someone is after Eve's power.

Eve has been captured, and placed inside a machine called Eden. Sven and Rinslet talk to Tearju, Eve's creator. She explains about The Eden Project. The goal is to eliminate violence and greed by using nanomachines to control humans. Can Train and the others save Eve from her fate?

As Eden rains down nanomachines on a city full of people, everyone else tries to think of a plan to rescue Eve. Chronos and the Apostles of the Stars team up with Train and the others, and come up with a plan to lure Eden to the ground. Will they succeed?

As Chronos and remaining members of the Apostles of the Stars fight the monsters outside Eden, Train and Sven go inside to rescue Eve, determined to save her even if it would cost them their lives. While Sven tries to get close to Eve, Train has to face off against his own inner demons first.