The series opens with a view of a large island facility, almost a fortress, and a helicopter landing on it, with a serious-looking man greeted by a bespectacled man waiting on the ground. The scene switches to inside the facility, and two guards waiting nervously inside a room fronted by a large reinforced steel door with many locking mechanisms. They are standing before an odd cage with someone bound up from head to toe. One comments and the other agrees that something is in the air, just as it was when another fellow guard died. The superior officer reminds the junior that security is currently weak even before a transportation expected the next day and that they cannot afford to be lax in their efforts. A brief flashback follows, showing how something as simple as a dropped pen led to the death of the guard mentioned before, though his death and the exact manner of it are not shown.
The bespectacled man takes the guest who arrived on a tour of the facility, warning him not to get within roughly two meters of the woman he has come to see, and also warning him to deposit any loose articles with security, again relating the incident of the guard who dropped the pen. The guest expresses disbelief and doubts that the area he is shown, a large steel structure some twenty meters underground, is a wise use of taxpayer money. The guide tells this man, now identified as a Vice-Minister of the Japanese government that he will soon see that, far from being a waste, why even more funds are needed even as they transport the woman in question into an even more secure location. The guide relates that the girl/woman is a mutant, with genetic differences that put her even above most born like her, and that worse, her birth appears to be no accident, but the choice of a higher power that wishes to replace Humans, just as modern Humans displaced their predecessors. When the Vice-Minister asks how she is different, the guide shows the captive, explaining that she has powers beyond Humans, and plans on replacing them with her kind, which he calls Diclonius.
At the Gokurakuji Train Station in Kamakura, a young man exits the train and recounts how the local college was the only one he was able to get into after several failed tries, and that now he will stay at his cousin's house nearby while at college. He takes in a whiff of salt sea air as he walks, wondering if his cousin will meet him, and what she looks like now since he cannot remember her face. The young man, named Kouta, is greeted by his cousin Yuka, who seems to remember him very well and smiles broadly to see him. Yuka expresses happiness that they are both going to the same university. They decide to refer to each other simply by name (minus honorifics like -kun-, -chan, or -San) and Kouta has an intense flashback of Yuka pleading with him not to forget her, which he obviously has done. Arriving at the sea, he takes the time to marvel at the sight.
At the Island facility, the Vice-Minister is thrown at the sight of the 'mutant,' encased in a cage that is just larger than her two-meter power radius, with noise resulting from her hitting the floor with that power since the floor is within her range. The guide takes the Vice-Minister upstairs while the move of the captive begins. In a moment that temporarily breaks the tension, a young woman enters the room where they have relocated to, falling over as she informs him that a Minister Kakuzawa placed a recent call, tripping a few times again after she is thanked and withdraws. The guide relates that she is his secretary, and while a capable graduate of Tokyo University, she is plainly not ready to deal with her work environment.
Inside the transit elevator, the guards grow ever more nervous as the captive keeps banging against the floor, till the junior officer is surprised by his cell-phone ringing, with the superior wondering how any signal can penetrate the depths and steel that surround them. One of the shocks from their prisoner causes the cell-phone to fall within her range, enabling her to seize and then sever the guard's arm when he reaches for it, then beheading him and taking his control keys and card while the senior officer watches in horror. His attempts to stop her with gunfire prove futile.
The clumsy secretary from before is fetching coffee when she is asked by her fellow secretaries about the scary reputation of their boss, Director Kurama, the name of the bespectacled guide. The secretary defends her boss, chastises herself for not being a better secretary, but vows to become the best she can out of devotion to him.
Two more guards await the transport elevator holding the prisoner. They see it open up to a scene of carnage and terror, with the freed captive standing naked amidst the body parts of the guards and wreckage of her cage inside, holding the head of the senior officer, her face still hidden by a restraint helmet. In his office, Director Kurama shows the Vice-Minister a scan of their captive's pineal gland, said to be the source of the legendary sixth sense in Humans, wedged up against the frontal lobe and as large as an egg in her case, indicating something extraordinary at the cost of possibly damaging her mind. Kurama states that if she spends her life at the facility, the new breed will die on the vine and provide valuable scientific knowledge, while her possible escape means the likely extinction of Humankind. A sudden alarm from an out-of-contact console room tells Kurama that the worst has happened and that the captive, whom he identifies as Lucy, has escaped her confinement chamber and is loose in the facility.
To make matters worse, Kurama's clumsy secretary Kisaragi has returned and encounters Lucy, who promptly takes the confused, scared woman hostage, demanding access to the outside hatch under threat of Kisaragi's life. With a clear shot blocked by Kisaragi, and needing to keep Lucy inside at all costs, Kurama sadly informs Kisaragi that her life must be sacrificed to prevent Lucy's escape. Kisaragi's devotion to Kurama is such that she finds a form of joy in the fact that she'll be helping him with her death. Lucy responds by tearing Kisaragi's head off and using her body as a shield against the hail of gunfire that follows. This grisly sight demoralizes the stunned guards and also slows some of the bullets enough so that Lucy can hurl them back to lethal effect against her attackers. One guard foolishly rushes her and has his heart torn out. Another is torn to pieces, terrifying and striking fear in the other guards, who ignore Kurama's urgings to stand firm. The door to the outside hatch then mysteriously opens, leaving Kurama with Lucy's laughter and taunts that Kisaragi died a pointless death. As she leaves, Kurama orders the surviving soldiers back inside and orders a sniper to target Lucy before she can escape by sea. Though she is unable to deflect the heavy Fifty-caliber bullet the sniper is using, it catches her attention in time. She is only able to slow the bullet with her power, but it strikes the thickest part of her restraint helmet rather the unarmored back of her head. Her long hair and face briefly become visible, and while she plummets off the cliff side, Kurama is grimly confident that Lucy has survived. He orders an immediate search be made for her, while the Vice-Minister informs him that he took the situation at the facility too lightly before, indicating that he will recommend more funding for the facility. Kurama for his part issues an apology to the late Kisaragi and swears vengeance on Lucy over her severed head.
On Enoshima Island near Kamakura, Yuka tells Kouta that they used to play there on Yuigahama Beach a lot when they were children, and begins to suspect that he cannot remember those times, a notion he tries to laugh off. Preparing to take him to the house he'll be staying at while at college, Yuka offers Kouta some cookies she's been eating, only to suddenly tell him not to look in front of him. Standing there emerging from the surf, naked, shivering and looking very confused is Lucy, the girl who escaped the island facility. All three stand at a loss for words.
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