Aprile. Arato, studente del secondo anno di liceo, aveva una vita normale che trascorreva con i suoi amici Ryo e Kengo. Fino a quella sera. Mentre torna a casa dopo aver fatto la spesa, Arato viene attaccato da un hIE corrotto, ma una bellissima hIE di nome Lacia arriva in suo soccorso.

Dopo aver firmato un contratto con Arato, Lacia è venuta a vivere con gli Endo. Yuka, la sorella di Arato, ha accettato completamente Lacia e l'ha persino iscritta a un'audizione per modelle di HIE. Nel frattempo, Arato non riesce a nascondere la sua apprensione per la convivenza con una ragazza che sembra avere la sua stessa età.

Nonostante la consapevolezza dell'hacking analogico, Arato non può fare a meno di essere attratto da Lacia. In mezzo a tutto questo, Lacia viene "rapita" proprio davanti a Yuka. Arato è arrabbiato con la polizia e con la sua riluttanza a trattare questo caso come qualcosa di diverso dal furto di proprietà, così chiede l'aiuto di Ryo e Kengo per indagare da soli.

Kouka, la violenta hIE che si definisce la prima sorella di Lacia. Grazie al suo controllo sulla rete di anticorpi, sta progettando di compiere un terribile atto di terrorismo. Quando Arato viene a sapere che il suo piano sta mettendo in pericolo Kengo, si mette in viaggio per salvare Kengo con l'aiuto di Lacia.

Arato arriva al centro di promozione industriale che è l'obiettivo dell'attacco terroristico della rete anticorpi. Salendo le scale, vede l'androide politico Mikoto sviluppato da suo padre, che lo mette a disagio. Poco dopo, l'unità terroristica guidata da Kouka e un altro HIE di classe Lacia arrivano sulla scena. Sta per scoppiare una grande battaglia!

Arato riesce a salvare Kengo dalla calamità del centro di promozione industriale. Tuttavia, anche dopo essere tornato alla vita normale, si ritrova consumato da misteri sempre più profondi. Nel frattempo, alla Memeframe Corporation si inasprisce una disputa tra fazioni. In questo contesto, la hIE Methode di classe Lacia sta per fare la sua mossa.

Having made a contract with Shiori, Methode suddenly attacks Lacia while she is filming a commercial. As the circumstances surrounding Arato and Lacia are about to shift again dramatically, a new transfer student arrives at Arato's high school. Erica Burrows-the Sleeping Princess born in the 21st Century who just awoke from suspended animation, and Arato senses animosity from her.

Shiori puts her plan into motion. At this rate, Arato will lose ownership of Lacia. "Mr. Arato, please allow me to be with you." This unexpected plea from Lacia moves Arato, and he heads to Chubu International Airport to stop Shiori.

Arato is given two weeks of suspension after the fight between Methode and Lacia leaves him with paying 4.5 million yen worth of damages they caused. In order to apologize to his father Kozo who offered to pay half of the damages, Arato takes Lacia, Yuka, and Ryo to Tsukuba where a large-scale hIE experiment is being conducted.

Methode abducts Yuka right in front of Lacia. Arato and Ryo head to rescue her, but standing in their way are all of the hIE's in the experimental city who have been infected by Ginga Watarai to act like zombies. In order to get the hIE's to regain control, Arato and Ryo head to the administration center, but...

Ginga Watarai's death puts an end to the incident at the experimental city. During all of the chaos, Arato had revealed his feelings to Lacia which she accepted. Yuka has mixed feelings about this sudden new coupling within her household. Meanwhile, the security police and Lacia-class masters begin to respond to the ever-changing situation.

After being summoned by Erika to the Burrows estate, the Lacia-class hIE's fight entered the next phase. As each of them contemplated their next move, Kouka felt her possibility for a future quickly closing as she was being pursued as a suspect in the Chubu Airport bombing by the security police.

Kouka carries out an antibody network terrorist attack against the Next-Gen Society Research Center on her own. Kouka's overwhelming destructive power is streamed around the globe, inspiring fear and zeal to the masses. This was Kouka's path to her future.

Kengo is arrested by the security police in connection to Kouka's terrorist activities. Arato decides to save Kengo and gives Lacia the order. Following the plan she has devised, Arato finds himself face to face with the PMC “HOO,” the military group responsible for destroying Kouka.

Affected by Kouka's destruction, Snowdrop moved up her own plans, taking over the Mitaka transformer substation to secure a steady energy supply and bringing disaster to the surroundings. Arato and Lacia try to stop her, but Methode and Ryo stand in their way.

Lacia's secret is revealed. Arato is unable to handle it and steps away from Lacia. Defenseless on his own, he's captured by Ryo and Methode where he could do nothing but watch the monitor as Snowdrop spread her seeds of destruction.

Pushed by Shiori and Yuka, Arato decided to face Lacia once again. If his last order was still in place, Lacia should be trying to stop Snowdrop. With this thought, Arato heads towards Mitaka, a place which has transformed into an unrecognizable landscape by Snowdrop's power.

It has been two months since the tragic events in Mitaka. The world returned to some semblance of normalcy, and Arato and Lacia lay low as they prepare for whatever may come next. However, their brief period of happiness is disturbed after they are contacted by the super intelligent AI Astraia.

Super intelligent AI have spurred society to change. As the fight surrounding Arato and Lacia escalates, the leaders of the old guard discuss how they could maximize their own profits. Among the participants, only Erika Burrows expresses anger towards their foolishness.

The super intelligent AI Higgins. The core of Memeframe, one of the keys to humanity's future, and the creator of Lacia. Arato and Lacia traverse through a giant underground facility in order to contact Higgins. There they will find a future far beyond the human imagination...

Once again, Methode appears to stand in the way of Arato and Lacia down in the underground facility containing Higgins. They must also be wary of Snowdrop who had been sent there by a rival super intelligent AI. As the conflict escalates, Arato and Ryo try their best to fulfill their duties as representatives of humanity.

Snowdrop appears in the underground facility as some sort of hybrid between bird and person, a strange new creature created by a super intelligent AI which no longer needed humanity to exist. Lacia attempts to hack the cloud system that stores hIE behavior controls in order to stop Snowdrop. Her efforts would determine the outcome of the entire human race.

Arato and Lacia walk towards the heart of the Higgins storage facility in order to choose a future. The two act like one as they help and support each other. However, damaged from the intense battle, Lacia does not have much time left...