B: The Beginning is set in a future where scientists have tried to create the "perfect human" in hopes of keeping peace in the universe. After nearly achieving their goal through several children, the scientists send their "new humans" for further training where they are kidnapped by an evil organization set on using their powers to implement their own concept of a new world order.
Keith rejoins the RIS just in time to work a brutal double murder involving "Killer B". Then an unknown group steals a military vehicle for a rampage.
The RIS investigates a death that appears to be linked to Killer B, though Keith disagrees. Another body leads them to stake out a high-powered party.
Kaela battles the hackers as the poison gas release ticks closer. Keith drags Boris on a chase outside the city, pursuing Koku and one of the gang.
Koku and Keith both pay visits to the Royal Library. Afterward, Lily heads to Keith's apartment to discuss her thoughts on the Killer B case.
The team members grapple with the attack on one of their own, and the fact that there must be a traitor on the inside. Koku realizes who Canopus is.
After confronting Keith on the roof of the hospital, Koku agrees to meet him at a temple the next day. Keith is declared a murder suspect.
Minatsuki gives the OK for the others to attack Koku, but Keith intervenes to protect him. The RIS receives an ultimatum.
Eric implores Keith to return to the RIS, then suspends Lily in an effort to track Keith down. Minatsuki sends Takeru after Koku.
Keith turns himself in and the RIS decides to spend the few remaining hours laying a trap for the suspected head of Market Maker, using Lily as bait.
Koku searches for the zeppelin containing Market Maker and Yuna. Meanwhile, Keith, Eric and Kaela frantically search for Gilbert and Lily.
Keith sets off in pursuit of Gilbert once more. Koku finds the zeppelin and Minatsuki, but Laica escapes with Yuna in accordance with the prophecy.
The RIS races to the scene, while Keith confronts Gilbert at the old Jaula Blanca facility. Koku fights Laica for his and Yuna's survival.
Koku is approached by Kirisame, a figure from his childhood who he thought was dead. He asks Koku to join him in his fight for a new world order.
Kirisame's subordinates force Koku into carrying out an act of violence against a senator. Then Koku breaks into the royal palace.
The royal palace refuses to fully cooperate with the RIS investigation. Lily and Koku head out to get more information on Keith's disappearance.
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Keith's friends narrow down possible locations where he's being held, but with Keith already starting to hallucinate from hunger, time is running out.
Koku, Izanami and Yuna have to fight off an ambush from Kirisame's subordinates. Lily gets pulled over while driving with the king in her car.
With the RIS continuing their pursuit of Killer B, Koku goes into hiding, but Kirisame seeks him out for a final confrontation.