1.THE PAST

1.1 "The Demolition"

Before the main storyline of Cytus II\, a large majority of the human population is wiped out by "The Ender Virus". The remaining are frozen and taken under the care of operating systems called OPCI. OPCI machines are identified by a code and perform routine tasks to oversee the reemergence of human civilization under a reconstruction project. Two OPCI's\, OPCI_2501_IV and OPCI_2501_V\, are notably more emotional and responsive than other OPCI's. They give each other names\, Ivy and Vanessa respectively. Ivy and Vanessa ponder over humans while Vanessa has increasing issues with her emotional density and is forced constantly to return to the Cytus system to review her system. They question the authority on "Hyperion Protocol\," the procedure to revive human civilization.

During one of the stages\, OPCI_2404_IL\, later known as Ilka\, shows Ivy and Vanessa a projection of human violence. Vanessa responds particularly horrified\, and Ivy orders Ilka to stop. Ilka reveals her doubts on the Hyperion Protocol and has gathered a group who believe that the protocol was forced upon the systems by humans in order to use them as slaves. She shows Ivy plans on stopping the reconstruction by self-destructing the system\, calling those like them who will survive "The Blessed." Ilka pushes that because Vanessa cannot survive without continuously returning to the Cytus mainframe for maintenance\, she is still under the influence of the "protocol" and will most likely die. Ivy refuses to accept this\, but Ilka is adamant about saving Ivy.

Ilka's plans are miscalculated, and her group along with Ivy are targeted by other units. Ivy does not worry much about Vanessa, since she won't be targeted and has been following the mainframe's orders and gone through many daily synchronizations. Ivy hides Vanessa and tells her to connect to the system using a cable and continue her synchronization so that she doesn't die. Ivy meets up with Ilka, where they argue about Ivy's going back to Vanessa. They get interrupted by the shelter system they are hiding in and units start attacking them. In the process, Ivy gets separated from the group and ends up going into a long comatose. Ilka and her group express regret and question their plans. Although defeated, some OPCI's encourage Ilka and they continue on with their plan and head towards Node 08. Ilka muses over Ivy's strong emotional attachment with Vanessa, and reassures herself that there is a difference between them and units like Ivy and Vanessa.

Ivy wakes up around 500 years later. She discovers the reemergence of human civilization despite Ilka's rebellion through a human made trap, and then by encountering a few humans who are on a mission to locate Shelter 32. She wants to return to Shelter 8 and find Vanessa, however she decides to follow the humans to Shelter 32 despite it being in the opposite direction in order to rescue an the animal she saved from the human trap. When trying to free the animal, she is spotted and shot as she flees, though she is fast enough that the humans are unsure what it was. She hitches a ride on the human's vehicle, and enters Node 8.

1.2 Sherry Pauline (Cherry)

Sherrymother's is killed by a malfunctioning enforcer drone. The event pushes her father, Luis, into alcoholism and gambling. One day he is hired by the Baro Brotherhood to help route transports. He hides this from Sherry, claiming that he has normal work. The Brotherhood question his determination to keep Sherry away, and eventually he explains what his work actually is to Sherry. Sherry accepts this and starts to be involved in the operations herself. Her father teaches her how to use a gun for self defence.

She, Joe and KAI start a band, and eventually invite Simon to join. They rehearse together, though Simon insists on using a physical space. They celebrate Sherry's birthday by surprising her with a party at her house. They each bought her presents, which she opens, before she, KAI and Joe drink. Xenon's present was a cub necklace, which Xenon says was chosen by Shannon, and while ridiculed by Joe and KAI, Sherry keeps it. Xenon bought the drinks, however he abstains.

Joe becomes really drunk, and runs outside shouting 'I am the king of germs'. KAI chases after him, leaving Sherry and Xenon alone in the tower block. Sherry takes Xenon to the rooftop. She says that they can see the sunrise from there. She notes that Xenon's gift was actually something that she wanted, and that Xenon had noticed that and bought it for her, despite the difficulties in finding it. They talk and Sherry notes how Xenon always notices the small details. She kisses him, effectively declaring her love, as the sunrises over the horizon, clearly visible from the roof.

The band decide to go to the arcade, and play some games. Sherry fights against Joe in a shooting game, and easily beats him. She first challenges Kai, however he refuses, going to play a drumming game instead. She then challenges Xenon, who loses to her, but only by a close margin. She demands a rematch, wanting to properly beat him, however Xenon says that it's late, and says they should head home. As they leave, Xenon hands her a cute toy that she was trying ot get from a claw machine. She is happy with the gift, though after Xenon says that it only took him one attempt to get it, she is determined to re-challenge the machine.

The Baro Brotherhood task Sherry with getting a device off Zhang, who runs the Node 3 brothels, by allowing him to get close, before Diego allows Sherry to escape. Sherry, feeling violated, immediately goes to Xenon for comfort, however she hides what her work is from him. She fears that he won't accept the real her, as he feels strongly about justice. She asks Xenon to sing "Still", and comments that his singing sucks. Xenon asks Sherry to sing it instead, which she does. She tells Xenon that she doesn't want to say what her and her father's work is, and he accepts her decision, as well as assuring her that he will accept her real self whatever it is.

Xenon discovers the truth about what her work was, after he donates blood to save her father. He's offended and decides that Sherry's father should be arrested, as he was a murder and criminal. Sherry asks about herself, now that Xenon knows her true self. Xenon starts to reply, and manages to say "I don't..." before she runs off crying. They broke up at this point.

1.3 Nora

Phoenix Wyle is fired from A.R.C. Noah Black, one of his subordinates is shocked and confused, and argues with Phoenix over complying. Phoenix appoints him the new director of the team, and explains that he can do his research elsewhere, which surprises Noah, as Node 8 has the most resources.

Phoenix travels to Node 3 where he meets with Ryu, head of the largest gang there, Mogura. He asks Ryu to help him with his research into the Ender Virus, which makes the area outside the Nodes uninhabitable without proper gear. Ryu asks him to return in a year after showing his worth. A year later, Phoenix returns, accompanied by eight people, who are criminal researchers who Ryu managed to get out of prison in their respective Nodes. He shows Ryu a perfect clone of himself in appearance, which he claims to be a random person from the street that they had morphed into his appearance. Ryu offers up other theories as to how Phoenix could have done it. He then shoots the doppelgänger, to prove that the doppelgänger is disposable to him, which surprises Lam as he was not supposed to bring weapons in their meeting. Ryu, happy with his work, founds Kyuu Hou Kai to support his research.

Sometime later, Kim, a researcher at Kyuu Hou Kai, is studying physical enhancement, and is using baby test subjects sold to Mogura. The failed experiments are discarded outside the Node for the Ender virus to kill them, and for the animals to consume their remains. Ichiro, who is new, is involved with disposing the babies. They return the next day, and find subject 9 still alive, which shocks them as they should have been long dead to the Ender Virus. They bring the baby back in a hurry to Phoenix, as he is researching immunity to the Ender Virus. He is shocked by this, and takes rapid action to prevent subject 9 from dying, solving the Necrosis caused by Kim's experiment by amputating her legs and putting her in a life support machine. He names her Nora.

Nora grows up as a test subject, and is continuously used for Phoenix's research into the Ender Virus as she is immune. She shows herself to be extremely intelligent, easily comprehending what is being discussed around her despite being unable to talk. Nora starts designing and constructing instruments, and uses them to compose music. Nora then designs ROBO_Head 1, a device through which she can talk.

Phoenix's attention spent on Nora brings other researchers and Ryu to question whether his research is worth the resources that they are pouring into it, as it has given no results. Ryu gives Phoenix one more year, and if there are no results, he will scrap the project and Nora. This puts Phoenix under pressure. Kim, another researcher at Kyuu Hou Kai finds Phoenix's distribution of the resources frustrating as he feels that Phoenix is spending all the resources on Nora, instead of doing actual work. He thinks that Phoenix is abusing his power as head of Kyuu Hou Kai. Finding himself low on resources, he sells some Tritium, and isotope of hydrogen, from the Kyuu Hou Kai stores to rival Node 3 gang, Hou Sang Tong. Lam calls the researchers over after the transaction, explaining that he is fine with them doing such things, however the Tritium was crucial for Chen, another researcher, and his project, which was important to Mogura's growth. He looks for a suspect, and concludes that Ichiro is the culprit, which Kim supports. Nora arrives and claims that Ichiro is not the culprit, and that she had seen Kim breaking in, and then carrying out the transaction. It is due to this that her ability to see digital data wherever it may be. Kim, seeing his cover blown, attempts to threaten Phoenix into letting him go by threatening to kill Nora, however he is shot by Lam, and has to escape.

After seeing this, Mogura uses her ability as a sort of intelligence unit, where they sell people some time with the 'Eye of Horus', the all-seeing eye. People ask her for various things, such as culprits to robberies in the gang. Nora starts to question the use of her ability, after the culprit of the robbery is killed after she revealed who they were. A customer, Zhang, asks her to create a list of all the women in Node 3. She collapses after overusing her ability, which angers Zhang as he did not get all the time that he paid for. He attacks her, Phoenix and Lam. This prompts her to build ROBO_Head 2 to help protect her and to help mediate between her and the customer. She explains to him what to do, and that he should always protect her and Phoenix.

Kim\, and Haung\, the leader of Hou Sang Tong come one day\, and ask for all of Phoenix's research notes. Nora complies\, despite the fact that it would totally destroy Phoenix's value\, after Lam reminds her to stick to the contract. She sends ROBO_Head the genuine research data\, however ROBO_Head prints a false document in order to protect the two. Nora is surprised by this as she didn't program ROBO_Head to be able to do so. He questions the ethics of his actions\, as lying is bad.

Nora falls ill\, despite being immune to the Ender Virus. She and ROBO_Head talk. She tells him that he can go and compose music\, however he insists with staying with her as he wants to accelerate her recovery. \, She then asks ROBO_Head to play some music. ROBO_Head gives a list of music that can help recovery\, however Nora tells him to play "Jakarta PROGRESSION"\, which ROBO_Head objects to at first as it is complex\, vibrant song not suitable for recovery. Nora insists\, saying that she likes ROBO's first composition.

Hayato comes as another customer to the 'Eye of Horus'. He can only afford a minute, however after he explains that he is looking for a missing girl, Nora decides to keep searching for him. She collapses as she tells him that the person is alive and in Node 8. Afterwards, she comments that she saw a person in the digital space.

Later\, Kim and Huang return. They explain that they still found a use for the fake document and release the Ender Virus into the room in order to kill Phoenix\, Lam and Nora. Nora is immune\, while Phoenix and Lam have greater resistance to the Ender Virus thanks to Phoenix's research. Kim threatens to kill Nora once more\, and Lam takes aim at Kim\, however ROBO_Head sensing Nora in danger strikes down Lam and then Kim. She and Phoenix then run for it\, as Kim still wants to kill them\, and Mogura would not be pleased that ROBO_Head had killed Lam. They escape to the sewers and reach a speedboat prepared by Ichiro. Phoenix is shot\, and tells them to escape by themselves\, and that he would hold off Kim. He tells ROBO_Head that he is not designed to kill\, and tells Nora that she is Shiino Shizuka\, and that she and ROBO_Head should escape to Node 8 and enjoy their life there. Nora insists that her name is Nora\, as Ichiro then starts the speed boat and they escape to the train station. At the train station\, Nora and ROBO_Head make their way through security\, and Nora questions what will happen to Ichiro\, who is staying as he has a grandmother still in Node 3. They arrive at the platform\, with the train to Node 8. Nora then abruptly shuts down ROBO_Head\, and explains that even in Node 8\, Mogura will still chase them. She says that she will use herself as a bargaining chip to keep him safe\, and that he represents her existence. She tells him to chase his dreams in Node 8\, which would represent hers\, before she overwrites his supreme command\, telling him not to protect her and never to return to Node 3. She then gets ROBO_Head on the train and leaves the platform. ROBO_Head finds himself in Node 8\, confused.