In a lab facility behind glass panels, AutoReivs, with the guidance of scientist Daedalus Yumeno, are experimenting on the specimen called "proxy". It begins to awaken, and sedatives administered are proving ineffective. It breaks out of its chains, then crouches and shatters the glass as it screams, while all the personnel are being evacuated from the lab as they try to contain the proxy.
It is 21:32pm as Vincent Law turns off his alarm clock and prepares for work. He drives off into the night before crashing suddenly, lying collapsed on the road. A mysterious figure appears and starts to narrate about "the malice implanted by the creator".
Inside Raul Creed's office, Raul is canceling his schedule before Kristeva, his entourage, enters and curtly explains that the Ultimate Level Intelligence is going to be disclosed. Raul stands up, and they leave his office.
Inside an abandoned warehouse, Vincent Law is firing at an infected AutoReiv while defending himself against an armed machine that was also following the AutoReiv. After destroying the AutoReiv, Vincent gets knocked out.
Daedalus Yumeno confirms to the Regent and four AutoReivs (that look like large statues) what happened back in the lab facility. One of the AutoReivs responds "We'll leave the rest to Raul", ending the conversation. The same AutoReiv then asks the Regent if Re-L is going to show up tonight.
Inside Re-L's car, Iggy, her entourage, toggles with the music player and asks Re-L questions, mainly about if she went to Regent Donov's last night and the spot searches around the city. For most of the ride, Re-L remains quiet and looks through her notebook. Soon she instructs Iggy to go to the FG Temporary Immigrant District's AutoReiv Facility.
At the FG Facility, Vincent is talking with his entourage, Dorothy, about the PK30-type AutoReiv, which he destroyed last. Seeing as Vincent couldn't verify that it was infected, Dorothy says that she will submit an intent to escape report instead, and then begins to brief him on his next infection to investigate. Whilst this occurs, Vincent pours milk into a bowl with alphabet cereal, and accidentally causes it to overflow. Vincent is shocked to find a row of letters appearing, forming the word "awakening".
Re-L enters the room, and tells Vincent not to rely too heavily on his entourage, as they are merely machines. She advises him to work harder on his human relationships if he wants to become a fellow citizen one day. Soon, Vincent leads Re-L and Iggy to the body of the infected AutoReiv from last night. Re-L comments on the state of the body and Vincent explains, handing her the hippocampus file which she then passes on to Iggy for analysis. She tells Vincent to discard his mosk necklace and not to bring it to his hearing. Iggy exclaims that they are in luck, because part of the autonomic nerve from the AutoReiv escaped infection, and based on its memory he was able to form a projected escape route. Re-L dismisses Vincent as she and Iggy leave. Iggy comments about Vincent "staring" at Re-L, which she quickly counters and lands on a photo of Vincent, glancing into the next room. She comments internally that his face is one of a fellow citizen that this town desires, a dull face. Shortly after, they leave the facility.
Inside Raul's office, Kristeva informs Raul that the area included within the Proxy search hasn't turned up anything, and that the armed AutoReivs patrolling the main land haven't found anything yet. Raul suggests that they should no longer presume it's in the residential area, and Kristeva walks off to makes the changes.
At an Immigration Bureau facility that is no longer in use, Iggy and Re-L begin to investigate. They barge into a room to find an immigrant and his Entourage, Mary, and Iggy identifies her as an ED26731 Companion AutoReiv. Re-L wanders off, and the proxy, the specimen that escaped from the lab facility, attacks Re-L. She blocks the proxy's movement and fires twice with her gun but misses both times, and it flees out the window, leaving behind an indent of its hand print. Mary appears, kneeling on the floor while lookign upward and holding her hands together as if she's praying, then she leaps from the current level all the way to the ground. Re-L has Iggy get the disposal unit to go after her, meanwhile she wonders what the proxy was.
Vincent injects a substance into Pino, to see if she has been infected with the Cogito virus. Raul's wife tries to say otherwise, when Vincent says that there isn't anything wrong with Pino. She gets angry and begins to speak rudely to Vincent before Pino interjects, silencing the wife's babble. Vincent packs up and leaves the house before Dorothy rings him.
Raul meets up with the Regent and they discuss the proxy problem and the search. Raul asks for permission to kill it, but is denied.
Iggy declares that he has found four dead bodies around the facility and Re-L attempts to explain about the monster that attacked her. The security bureau momentarily take control over Iggy as they press an order: "any continuation of this activity may constitute a violation of official regulations." Re-L replies, "Yeah, I know. They told us to safeguard the crime scene, but they never said we couldn't look around." They leave the scene.
Daedalus takes Raul to the lab where the proxy broke out to analyze the scene. Raul questions Daedalus but receives no answers to his questions, as he says he doesn't know the answers himself. Kristeva tells him about Temporary Immigrant District D and Re-L Mayer, whom is around the area.
Iggy drops Re-L off home before leaving to access the database at headquarters as Re-L instructs. Re-L reclines in a chair and thinks about the day that has transpired. She begins to undress to ready herself for a bath. Back in the car, Re-L's notebook falls open. Iggy notices and he turns the car around to head back immediately.
Re-L turns the water on, and as the mirror steams up she is shocked to find the word "awakening" scrawled across it. As she turns around, a different proxy appears, crashing through the roof. He interacts with her before the escaped proxy enters, and the two clash. Re-L loses consciousness while the two are fighting.