| ShortSummary
| - The sweeper alliance gathers at a port before heading to Creed's island. It turns out the leader of the alliance is really Number X, Lin Shao Lee, and that Chronos has hired them to act as decoys. Dr. Kanzaki releases nano/Tao beasts on the city, and the sweepers defeat them. They and Chronos decide to work together and fight against Creed.
- During a conversation, Creed tells Durham that he is no match for Train leaving him irritated. While searching for a criminal, Train's group discovers that their target has already been captured by a man impersonating Black Cat. Eve meets such person, Woodney, and it turns out that he is using such identity to scare people who want to bother him. Still, Eve befriends Woodney and secretely defeats a trio of people wanting to defeat Black Cat before they proceed to attack Woodney. Meanwhile, Jenos finds Rinslet and requests her to stop pursuing the Apostles of the Starts though she denies doing that as she wants to find the Tao potion. When Rinslet and Sven search for Creed's group alone, Durham finds and treatens Eve to know Train's location, but Woodney tries to protect her. Train then encounters Durham and easily defeat him. Next day, with Woodney's help, Train's group make Durham tell them Creed's location.
- Before escaping on a helicopter, Charden tells Train that he can meet Creed in the San Geles City. During a political gathering from such city, Creed and the Apostles of the Stars start a terrorist attack as part of their plan for a revolution. When Train finds and threatens Charden and Kyoko, Creed appears before him. Creed once again requests Train to join him, but Train tries to kill in revenge for Saya's death. All of Train's bullets are blocked by Creed's sword and when he manages to pierce a bullet through his chest, Creed easily heals his body with Tao's power. When Creed's partner Durham Glaster shoots Train, Sven receives the shot, and Creed leaves frustrated. Train firously asks Sven why did he get in the middle of the fight, but Sven hits him for fighting alone. Rinslet then explains to Train that Sven's best friend was a comrade from the FBI and died in a battle for protecting Sven, causing him to be afraid of losing his partner with his right eye being the one from his friend. Next day, Train and Sven make up by having a childish fight.
- Train and Sven successfully enter Eden and fight their way through their defenses, but they meet Mason. Creed shows up to fight Mason while Train and Sven go to save Eve, but Train meets Zagine's ghost due to Eden tampering with his past memories. After some talking Train severs the link between Eve and Eden and everyone returns to their lives. Rinslet is with Jenos as Sven and Eve drive off looking for Train, who disappeared after the battle; they are confident in that he will join them again eventually. In the end, Train walks into the streets thinking of Saya, with a smile on his face.
- With Rinslet, Sven goes to rescue Eve. Train easily defeats most of Torneo's men, but Sven is able to get to Eve before him. As he catches up with him, Train tries to shoot Eve, but is punched by Sven who escapes with her. With Eve having decided to join Sven, Torneo activates a device planted on Eve that turns her into a monster by controlling the nanomachines inside her body. As Eve is ordered to kill Train, Sven manages to escape from Torneo's men with Rinslet's help. Sven removes the device at the cost of being stabbed. Train then destroys all of Torneo's experiments, collapsing his castle. While Sven is healing, Train once again attempts to shoot Eve but decides not to do it remembering Saya's way of life.
- Sephiria orders Train to dispatch Creed, but Train declines, wishing only to apprehend him as a sweeper. During their battle, Train, with help from Saya's spirit, fires an orihalcon bullet into Creed's fully-awakened Imagine Blade, shattering the weapon and defeating Creed. Eve disables the nanomachines within Creed, who leaves with Echidna Parass. The heroes win the battle, but it appears some of the Numbers and Apostles have betrayed them.
- The nanotech bullet has changed Train into a young boy. Eve and Train meet Tim, Layla, Mika and other orphans, and they help them fend off a group of gangsters. Train's past, where his parents were killed by an assassin who raised him, is explained.
- Sven arrives at Torneo's mansion as Train is about to shoot Eve. Torneo's men interrupt them, forcing Sven and Train to escape. The next day, knowing that Rinslet is not Eve's older sister, Sven confronts her concerning what she really wants. Rinslet explains that Eve is a genetically engineered bio-weapon and that she wants to take the data from Torneo's experiments. Sven runs into Eve, who escaped from Torneo, at a park and befriends her. As both eat an ice cream, Eve is re-captured by Torneo and Sven decides to rescue her. That night, Train and Sven devise a plan to attack Torneo's mansion.
- Sephiria fights Train but both are interrupted by one of Creed's comrades, Shiki, as Creed still wants to make Train become his partner. They escape when Saya's song dispels his magical insects. While returning to his house, Train starts playing with Saya who returns Hades. Saya then arranges to have a date with Train to watch the fireworks during a festival that will be celebrated the next day. Enraged with how Train is changing, Creed leaves a note in Train's house the next day, which has him running desperately to find Saya. Before the date, Saya is attacked by Creed, but is only able to stop him from killing children from the festival. Train attacks Creed before delivering the final hit on Saya, who still dies happy that she was able to see fireworks with Train.
- After having a nightmare of Saya's death, Train goes to Creed's castle. At the same time, Jenos and his partners Beluga J. Heard and Naizer Bruckheimer, locate and attack Creed's castle in order to kill him. The three Chronos' Numbers are attacked by the Apostles Kyoko, Leon Elliott and Maro, but they manage to defeat them by attacking them with the first floor's roof. While continuing their pursuing, Charden, Echidna Parass, and Shiki confront the Numbers. Sven, Rinslet and Eve enter into Creed's castle, but Eve separates from them to rescue Leon and Rinslet and Sven are captured by "Doctor". Train gets to Creed, and both fight once again. During the fight, Creed requests Train to shoot him in his head so that he may recover his assassin nature. Train does so but Echidna blocks the bullet. Jenos enters into Creed's room, but he falls from the castle due to one of Creed's attacks. Beluga shoots the castle with his bazooka until making it collapse, making the captured Sven and Rinslet also fall. Before continuing fighting Creed, Train decides to save his friends instead of seeking revenge and Creed is ambushed by Naizer and Beluga. Later, in Sven's car, they talk about why Train saved them instead of getting revenge. Somehow he conversation leads to Saya, and Sven asks if she was Train's girlfriend. After a few seconds of thinking, he says that she was just a close friend. However, Eve doesn't think so and states that Train got dumped.
- Mason, along with a few traitorous Numbers and Apostles, has formed the Zero Numbers. They have a plot that involves taking Eve to Eden, a giant experimental machine. They kidnap Eve by placing a device on her that removes her personality and makes her an unemotional weapon.
- The condition of Chronos wanes as Creed reveals its existence and the corrupt nature to the world while he seeks media attention. The Numbers grow restless, and Sephiria moves in to seek answers from, and even to kill, Train. However, Sephiria is interrupted as Charden interferes and combats both. Afterwards, Sephiria gives Train an orichalcum bullet to use later.
- Creed kills Durham, which influences Charden's and Kyoko's decision to leave the Apostles. Kyoko decides to make Train a chocolate for "Heart Gift" day. Doctor Kanzaki shows up and tries to shoot Kyoko with a nanotech bullet, "Lucifer," but Train jumps in front and is hit.
- Rinslet goes off in pursuit of Charden and Kyoko while Train's group go after a Gyanza criminal enhanced by the power of Tao and who was arrested by Sven seven years ago. Train temporarily leaves the group in search of milk, and meets Kyoko, who falls in love with him after he saves her from a gang in the moment she was about to kill them. Train ignores her and returns to the group to prepare to capture Gyanza. Sven disguises himself as a woman to make Gyanza attack him. In the course of the fight Kyoko is involved, but she avoids all of Gyanza's attacks. By using his right eye, Sven helps Train to defeat Gyanza. Charden then comes and introduces Kyoko and himself as Apostles of the Stars, a group created by Creed.
- Thinking that he is being used by Chronos, Train decides to leave the organization to start a new life. Chronos sends Creed Diskenth to kill Train, but Creed is easily defeated. Creed then asks Train to join him in a revolution against Chronos which Train denies. When Train leaves, Chronos' soldiers come to stop Creed, but he kills them furiously as they interrupted his meeting with Train. Train finds Saya, gives her his gun, Hades, and thanks her for helping him to decide to leave Chronos. With Creed being unable to stop Train, a high ranking member from Chronos, Sephiria Arks goes to confront him.
- When an enraged Train fights Creed, Eve smells the blood and asks Sven to take her to its source. A week later, Train wakes up in Sven's cabin as Sven and Eve found him seriously injured during the festival. Eve still does not trust Train because of his former life as an assassin, resulting in Train telling her that she is also a murderer. After this, Eve escapes scared from the cabin and she is found by the Chronos assassin Jenos Hazard who wants to finish Train's work. Train comes to Eve's defense and helps her to knock Jenos out, who still fakes his defeat to avoid fighting. Meanwhile, Chronos changes its focus to Creed, instead of Train. The next day, Train leaves with Sven and Eve to work as a sweeper.
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