The Chronos Number assassin known as Black Cat is assigned to kill Lib Tyrant, a mobster who has been elected governor. Meanwhile, a sweeper named Sven Vollfied also pursues Tyrant for the bounty on his head.
While Black Cat is brooding on a rooftop, he meets Saya, a sweeper. Later, Saya takes a job capturing Preta Ghoul, a murderer who can cause people to disintegrate by touching them. Meanwhile, Sven is hired by a woman to rescue her sister, who has been kidnapped by the arms dealer Torneo Rudman.
As Sven enters Torneo's mansion, he finds Black Cat pointing a gun at Eve. Before he can shoot, Torneo's men interrupt them, and both Sven and Black Cat have to escape. Later, they both learn of Eve's true nature, and Sven befriends Eve, who left the mansion.
Both Sven and Black Cat break into Torneo's mansion, each trying to get to Eve before the other. Also, Rinslet discovers Torneo's other bio-experiments.
Train fights Sephiria while Creed fights two other Chronos assassins, but the fight is interrupted by Shiki, a member of the Tao who works for Creed. Later, Train and Saya race, and they plan a date to watch fireworks. Also, Chronos discovers where Sven, Eve, and Rinslet are hiding.
Train wakes up a week after his confrontation with Creed, but his memory of the events is a little fuzzy. Sven, who is nursing him back to health, explains what happened, and Eve asserts her disapproval of helping Train. Later, Eve runs away and is found by Jenos Hazard, a Chronos assassin who has been assigned to kill her.
Train is now helping Sven and Eve with their sweeper jobs, and he and Eve compete with each other to capture their next bounty--Igor Planter, a criminal who shares a strong bond with plants. Also, Jenos Hazard hires Rinslet to retrieve a bottle of a Taoist potion that two strangers are giving to criminals.
Train, Sven, and Eve go after Gyanza Rujike, a rapist who Sven has arrested before. Meanwhile, Charden and Kyoko attempt to meet with Gyanza. Also, Train meets Kyoko, who falls in love with him.
While Sven, Train, and Eve look for a target, they discover that he has already been captured by someone who is impersonating Train. Meanwhile, Jenos requests that he be allowed to lead Cerberus against the Apostles of the Star, and he asks Rinslet to stop looking for the Tao potion. Also, Durham decides to go after Train.
Warning signals go off in Charden's head after he sees Creed kill Durham for disobeying him, so he and Kyoko leave the Apostles of the Star. Kyoko returns to her normal life, and she looks for Train. Meanwhile, the Apostles plot to kill Charden and Kyoko for their betrayal.
Sven and Rinslet investigate nanotechnology to determine a way to return Train to normal. Meanwhile, Train and Eve help a group of orphans fight against gangsters who want to force them out of the abandoned factory where they live and turn it into a casino.
A sweeper alliance is formed to capture Creed, and Sven meets with the alliance. Meanwhile, Train, Eve, and Woodney look for a rich woman's pet lizard.
While looking for a route to Kraken, Train loses his way in the mountains. He is found by Saki, a mountain-dwelling woman who bears a striking resemblance to Saya, and he attempts to discover what secret she is hiding.
After Train reveals to the sweeper alliance that their leader is actually a Chronos Number, they all must decide if they want to continue their mission to capture Creed. Meanwhile, Creed grows stronger with the fusion of nanotechnology into his body, and Dr. Kanzaki decides to unleash his newest creation--a group of bio-weapons that are powered by both Tao and nanotechnology.
Chronos and the sweeper alliance each begin their assaults on Kraken, and they fight Dr. Kanzaki's minions and the Apostles' soldiers. Also, Eve fights Leon and David fights Maro.
Mason reveals that he is the leader of the Zero Numbers, a group made up of rogue Numbers and Apostles; Rinslet discovers the existence of the Eden Project and tries to hack into its database; the sweepers celebrate their victory; Eve is kidnapped by Doctor Kanzaki after a dispute with Sven.
Mason watches as Eve begins to merge with Eden; Train recruits a group of old allies to help save Eve; Rinslet finds Tearju Lunatique, who created the Eden Project.
Eden continues to grow in size and strength as it is attacked by an army; Leon, Kyoko, and Charden join Sven and Train's group, which forms a plan to stop Eden and save Eve.
