During another night at the apartment, Misato listens to Kajis final message. He urges her to continue his investigation and also asks her to take care of his flowers, telling her that Shinji knows where his patch is. She remarks to herself that the phone will never ring again.
Shinji notices that Misatos got her door shut and locked with a sign outside. The same goes for Asuka, whos actually over at Hikaris house. Hikari actually feels anything but comfortable with Asuka, who just sits in front of Hikaris TV playing videogames all day, rarely talks, and refuses to go to school. Nonetheless, she still lets Asuka sleep over. As both of them lie down, waiting to fall asleep, Asuka tells Hikari that shes sorry for being a burden and that she just cant seem to bring herself to care about anything anymore. She cant pilot her Eva to do anything useful and for that she hates herself. Hikari tells her to not feel that way and that she should feel good for having done the best she could. Her words dont have an effect on Asuka, who starts to cry.
In NERV HQ, Ritsuko gets a phone call with bad news from her grandmother. It turns out that the cat Ritsuko left in her care has died. She tries to console her grandmother, promising to visit her as soon as she gets any time off from work, and that she will also take some time to visit her mother's grave, since she hasn't been by there for three years.
SEELE has a talk with Gendo. They are disappointed in the Lance of Longinus being thrown away into lunar orbit, evading all possible means of retrieval. Gendo, unmoved by their barely restrained hostility towards him, defends his decision by stating that his first priority was to destroy the Angel and he deemed using the Lance necessary to do so, but the council are not impressed with this explanation and they even begin to openly express doubt regarding Gendos loyalty, and even Chairman Keel admits that he is starting to become suspicious. Gendo, however, quickly bows out of the meeting when a urgent call for him comes in, leaving SEELE to fume about his insolence. The sixteenth Angel, Armisael, has arrived.
Armisael takes the form of a ring of light consisting of two bands interwoven together. The MAGI is unable to get a decisive reading on it, so Unit-00 is sent out to take point, with Unit-02 providing the backup. Asukas abilities as a pilot havent been any lower than they are now. Gendo moves Asuka out with the intent of possibly using her as a decoy. Inside Unit-02, Asuka stares numbly ahead, wondering why she agreed to show up, blaming herself for being bad at letting go of things. She notices that all she can do now is getting in the way. "I don't care anymore," she meekly mumbles.
The Angel seems to be just rotating above the ground, and it remains passive and stays in place, while the MAGI struggles to gather data on it. Ritsuko says that the Angel might be able to change shape, prompting Misato to warn Rei to stay back, as they are not yet sure what the Angel is capable of and they need to study it further. But Rei, sensing that something is wrong, answers "No. It's coming." Right then the Angel forms into a single-banded ring. As everyone watches, it breaks apart into a snake-like form and moves swiftly in a beeline for the Eva. Rei is too slow to avoid it and it effortlessly pierces Unit-00's A.T. Field and the Eva itself. Rei tries to grab on and shoot at it to no effect. The Angel begins to infect the Eva Unit and, in turn, Rei. Unit-02 cant even move due to Asukas low sync ratio, causing Misato to call her back into the command center.
As the Angel infects Rei, it makes contact with her mind. Rei wonders who it is thats trying to communicate; she considers if it is "the me inside the Eva", but realizes that the presence is something different and alien. She asks the vision inside her mind if it is the Angel. The Angel has taken the form of Rei in her plugsuit, standing in a sea of LCL while the real Rei floats above. The Angel asks if her if she wants to become one with it. Rei refuses saying that she would prefer to keep her singular identity. The Angel concedes her statement, but says that its already too late for her. The Angels infection is shown to be spreading, and through this it shares its feelings with Rei. Rei recognizes what the Angel is feeling. She recognizes it as loneliness.
The Angel asks what that is. Rei explains that she is a human and there are many humans yet only one Angel. The Angel is alone and thus it feels this way. But the Angel twists it around, saying that this same feeling is prevalent inside Reis soul as well. Rei comes back to reality and finds herself crying yet wondering why.
The infection starts warping the Evas body and Gendo eventually calls off the lock on Unit-01. Asuka bitterly notices that same wasn't done for her, bitterly saying: "Am I so worthless to you?", as Unit-02 is extracted from the field. Unit-01 arrives at the surface, and following the usual procedure Shinji extends the Eva's A.T. Field, but this instantly draws the Angel's attention, and it quickly slithers towards him through the air. In an attempt to hold it off, he grabs it, but the physical contact allows the Angel to spread its infection to Unit-01 and Shinji. He then stabs the Angel with the prog knife, only to hear it scream with a voice thats chillingly human. Visions of Rei begin to manifest in the bulging vessels of his hand where the infection is spreading and a white Rei comes out the Angels body, reaching out to Shinji, who is stunned in utter horror. "Does my soul want to become one with Ikari?", Rei wonders.
Rei then takes action and begins to spread out her A.T. Field to contain the Angel, tearing it away from Unit-01 and forcing all of the creature inside the core of Unit-00, causing the Eva's abdomen to swell up in what looks like a grotesque parody of pregnancy. Maya warns that the Eva's core has been pushed to its absolute limits and won't be to maintain the field for long, and Misato orders Rei to quickly abandon Unit-00. "No. If I go the A.T. Field will disappear. So, I can't" answers Rei as she determinedly activates the Eva's self-destruct mechanism. "Rei, do you mean to die?" asks Misato in utter disbelief. As the bulging core of Unit-00 collapses and begins to implode, Rei sees a vision of Gendo smiling. Unit-00 rises to its feet and reaches for something unseen, as it begins to shine and momentarily takes the form of a large white Rei with a halo over her head. The unit then detonates in a massive explosion, resulting in the destruction of the entirety of downtown Tokyo-3 and some of the surrounding area. Shinji can do nothing but watch from Unit-01 as the fireball grows out. After the Angel is confirmed to be destroyed, Misato, who is only barely keeping her voice from shaking, orders a rescue team to be sent out. Ritsuko quietly remarks that there might not be anything to rescue. Misato shoots her an absolutely withering look.
The ruined remains of Tokyo-3's downtown quickly starts to flood, as water from the nearby lake pours into the crater left by Unit-00's destruction. Around the edges of the crater, a decontamination squad headed by Ritsuko scour the area; they soon discover Unit-00's scorched and broken entry plug. The only thing found inside it is the charred remains of a body. Ritsuko orders that the team's finding is to be classified as top secret and for the plug to salvaged. Everything else is to be disposed of.
SEELE discusses the aftermath. After the sixteenth Angel, according to the Dead Sea Scrolls, there is only one more. The Lance of Longinus has been lost and now, with the destruction of Unit-00, they have more than enough reasons to remove Ikari from command of NERV. They point out that he ignored the warning they gave him by abducting Fuyutsuki, so they decide to use another person against him; this time, someone who knows the truth.
Shinji sits on his bed staring into space. When Misato comes into his room, he tells her that he cant cry anymore. He feels the pain, but tears wont come. Telling Shinji, "This is about all I can do for you right now," Misato moves to hold his hand, but he pulls away quickly as he tells her to stop it and turns his back on her. Misato wonders if its just her, or because shes a woman, or if he just wont get close to anyone. Misato, desperate for any company at all, tries seeking out Pen-Pen instead, but he just lies depressed around on the floor, and barely looks over at her when she calls his name.
Gendo and Fuyutsuki stand in front of the machine in Terminal Dogma which Rei steps into from time to time. Fuyutsuki remarks that Rei is the product of his despair and the vessel for Gendos hope. He says that he had hoped Gendo would be able to forget, but now just thinks that such a notion is unreasonable.
Some time later, Misato gets a call, telling her that Rei has been found alive. She runs to tell Shinji the news. Shinji sees her at the hospital ward, with her right eye bandaged and her arm in a sling. As he thanks her for saving his life, she seems not to remember it. She simply remarks that it must be because she is "the third one." She returns to her apartment later that day, and as soon as she is inside, she discards her bandages, revealing herself to be completely undamaged. Looking around she sees Gendos glasses on the table, picks them up, and begins to crush them. She stops once she begins to cry, yet she does not know herself why she is crying. She remarks that this is the first time she has seen these things, yet also not the first time.
Back at headquarters, Fuyutsuki remarks that SEELE is going to be quite surprised that Rei is still alive. Gendo waves the concern away, saying that he has offered SEELE something else. Meanwhile, Ritsuko stands, stark naked, in front of the SEELE holograms for an inquisition. Keel, playing good cop, encourages her to cooperate and answer their questions to avoid further degradation, but, attempting to play it cool despite the circumstances, she insists that she doesn't feel humiliated at all. The council commends her for her loyalty to Gendo, but reveals that he was the one who sent her to be interrogated when it actually was the First Child who was requested.
Misato finds a small chip inside the capsule that Kaji gave her at their last meeting. She remarks that with this, the pain of his loss no longer hurts since he has given her his heart and soul. After the inquisition, Ritsuko is set free. SEELE discusses the destruction of Tokyo-3, and notes that it might actually be a boon to their upcoming plans and decides to accelerate the production of the new Eva series even more, with Keel saying that the promised time will soon come. Ritsuko calls Shinji, telling him she has been able to lift the security restrictions placed on him and asks him to come over to NERV HQ. Later, Ritsuko stands before the lock to Terminal Dogma, only to discover that the access code has been changed. "It is no use. Not without my pass," says Misato from behind her as she points a gun at Ritsuko's back. Ritsuko guesses, correctly, that it is Kaji's handiwork. Misato demands that Risuko reveals her secrets, to which Ritsuko agrees as long as Shinji, who emerges from his hiding place in a nearby shadow, comes along too. Misato agrees resignedly.
Ritsuko guides them several floors underground to facilities dating back to the days of GEHIRN. She first shows them a room that reminds Shinji of Reis apartment. She reveals that this is where Rei was born and raised. She then takes them what Shinji calls an Eva graveyard but Ritsuko corrects him: its nothing more than a dumping ground for failed Evangelion projects, as well as the place where Shinjis mother disappeared many years ago. "You may not remember it, but you were watching when your mother disappeared," she says to Shinji, who is visibly shaken. Misato raises her gun as a warning, but Ritsuko just cruelly smirks back. Finally she takes them to the machine with the tube filled with LCL. It is the core of the dummy plug; the place where the components are produced. Ritsuko presses a button on a remote, turning on all of the room's lights. Shinji and Misato look on in shock and disbelief, as the light reveals an LCL filled tank that spans the entire circumference of the room, containing multiple bodies of Rei, all of them with a vacant, smiling expression on their faces. These are revealed to be what makes the dummy plug work. They are simply empty vessels, in Ritsukos words, lacking a soul. She then reveals to the others that the Eva are simply mans attempt at making a man with the power of a god. The Evas are biological constructs, created from biological material harvested from Adam, and has a human soul embedded inside, very much like Rei.
As soon as she finishes explaining, Ritsuko proceeds to press another button on the remote that destroys the bodies, disintegrating them. Outraged, Misato asks her if she knows what she just did. Ritsuko answers she fully well knows what she is doing and denies that the "things" in the tank were ever remotely human. She reveals her motive to be her unrequited love for Gendo. She says that even though these are just lifeless husks, Gendo still chose these, chose Rei, over Ritsuko. She then asks Misato to kill her, saying that she doesnt care anymore. Her voice breaks with tears as she falls on her knees, lamenting her foolishness. A foolishness she shared with her mother.
Misato does nothing but watch. She wonders about this "curse" that seems to affect everyone involved with Eva, including herself.
- Body Backup Drive: The big reveal of the episode is that Rei has one of these.
- Body Horror: The Angel's taint on Shinji manifests itself as small rapidly growing Rei faces. The infection itself manifests normally on the pilot as bulging veins crisscrossing across the pilot's body as well as their EVA.
- All of the Rei clones in the tank fall apart with the touch of a button.
- Heroic Sacrifice: Rei (II) sacrifices herself to destroy Armisael.
- Hotter and Sexier: The Director's cut gives the dummy Reis nipples, and the updated Renewal version omits the random images that flash during the sequence, allowing the camera to focus more on their nude forms.
- Really Dead Montage: Downplayed. To signal that Rei (II) is really going to die, she sees a short Happy Flashback of Gendo smiling at her, just before Unit-00 explodes.
- Talking Is a Free Action: There wasn't enough time for Rei to dodge Armisael's attack, but there was more than enough time for Hyuga to point that out.