During another night at the apartment, Misato listens to Kajiís 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 Misatoís got her door shut and locked with a sign outside. The same goes for Asuka, whoís actually over at Hikariís house. Hikari actually feels anything but comfortable with Asuka, who just sits in front of Hikariís 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 sheís sorry for being a burden and that she just canít seem to bring herself to care about anything anymore. She canít 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 donít have an effect on Asuka, who starts to cry.
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, and they are doubtful of Gendoís loyalty, and even Chairman Keel is starting to become suspicious. A call comes in for Gendo, however, forcing him to leave. The sixteenth Angel, Armisael, has arrived.
It 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. Asukaís abilities as a pilot havenít been any lower than they are now. Gendo moves Asuka out with the intent of possibly using her as a decoy.
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. Risuko 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 comming." 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 canít even move due to Asukaís 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 thatís 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 itís already too late for her. The Angelís 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 Reiís soul as well. Rei comes back to reality and finds herself crying yet wondering why.
The infection starts warping the Evaís body and Gendo eventually calls off the lock on Unit-01. Asuka bitterly notices that same wasn't done for her, mumbling: "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 thatís 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 Angelís 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, forcing all of it inside of Unit-00. Then, she begins the self-destruct sequence on the Eva, despite protests from Misato. As the bulging core of Unit-00 collapses, 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 Tokyo-3's business-district 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 barley keeping her voice from shaking, orders a rescue team to be sent out. Ritsuko quietly remarks that there might not be anything to rescue.
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, Ritsuko and a contamination squad 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, there should be sufficient reason to remove Ikari. 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 canít cry anymore. He feels the pain, but tears wonít come. As she moves to hold his hand, he pulls away quickly. Misato wonders if itís just her, or because sheís a woman, or if he just wonít 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 Gendoís 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 she must be 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 Gendoís 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 inside the capsule that Kaji gave her a while back a small chip. She remarks that with this, the pain of his loss no longer hurts since he has given her his ďheart and soul.Ē 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 down and takes him into Terminal Dogma. But when Shinji shows up, Mistao arrives along with him, demanding at gunpoint that Ritsuko reveals all her secrets.
Ritsuko first takes them to a room that reminds Shinji of Reiís apartment. She reveals that this is where Rei was born and raised. She then takes them to an Eva graveyard. It is a dumping ground for failed Evangelion projects, as well as the place where Shinjiís 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. Ritsuko just cruelly smirks at his reaction. 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. The room is then fully lit and in a tank that spans the entire circumference of the room, multiple bodies of Rei float with a smiling expression on their faces. These are revealed to be what makes the dummy plug work. They are simply empty vessels, in Ritsukoís words, lacking a soul. She then reveals to the others that the Eva are simply manís 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 a button 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 doesnít 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 ďcurseĒ that seems to affect everyone involved with Eva, including herself.
- 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.
- 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.