At this time, Instrumentality has begun. The exact time is unknown but Shinji, Asuka, Rei, Misato, Kaji, Ritsuko, Toji, Kensuke, Hikari, Ibuki, Hyuga, Aoba, Gendo, and Fuyutsuki converse and examine each other in a way that could only be possible with the melding of human souls that is Instrumentality.
After Kaworus death, Shinji is traumatized. Immediately after the event, as he sits outside the GeoFront, he tells Misato of how Kaworu, who was a much better person, should have lived. Misato gets him out of this train of thought by saying that Kaworu desired to die. He abandoned his will to live, and beings that do so have no reason to exist. Even so, Shinji is unsure of exactly why he killed Kaworu and tries to justify his actions by saying that Kaworu was an Angel and thus, an enemy. Of course, this is just another facet of the whole problem Shinji has in trying to figure out why he pilots an Evangelion in the first place. He asks himself and other people what he should do and where he should go. Should he still pilot the Eva even after being force to kill someone he loved?
The question is posed thus: Why do you pilot the Eva? Shinji answers it by saying that it is his duty. He was told to do it by his father and by everyone else around him. Thus, he does it for the good of mankind and everyone praises him for it. They treat him well because of what he does.
Asuka, begs to differ. She appears in front of him, saying that everything he has been telling himself is just a lie. All Shinji really feels is lonely. He simply wants people to acknowledge his existence by having them depend on him because of his skills in piloting an Eva. Shinji, thus, is really just piloting the Eva to satisfy his own selfish desire. Rei appears behind Asuka at this point, asking her if she hasn't had the same thoughts.
The focus switches to Asuka. She is sitting inside of Unit-02, floating in a large body of water. She sits in the entry plug, curled up and crying. She laments the fact that she can't control her own Eva and says that no one will need her anymore because of it. Rei's voice then remarks that Asuka is just trying to find her identity and value through what others see in her, something that Asuka denies vehemently. She is just trying to find and establish a strong independent identity with the Eva. Asuka is feeling afraid right now. The reason is because now she is losing the way through which she can stand out from others. Asuka tells Rei to shut up, sensitive about hearing those words from a "wind-up doll" like Rei.
The focus shifts once again to Rei. Rei III has a conversation with the other two Reis that have come before her. Rei I appears as child and a floating face. Rei II appears as Rei in her plugsuit. Rei III appears as Rei in her school uniform. The first issue that Rei deals with is her identity and whether or not she is false or fake. Rei III states that she exists and thus cannot possibly be fake, a bit like "I think therefore I am." Rei II expounds on this by saying that she has been formed through countless interactions with people. She has formed an image of herself in others through these interactions, but she has also formed an image of herself inside her mind through these interactions. Rei I brings up the fact that there is another part of the identity of Rei that the other Reis are ignoring. A "dark" part of her heart that might not still exist in human form, but if found, could mean the end of the existence of Rei Ayanami. She prods the other Reis, asking if they fear this. Rei III says that she does not fear. She would welcome death and nothingness. She wants to go back into nothingness, and would be able to if not for Gendo. Gendo desires her existence selfishly, and thus will keep her alive for as long as he wants. However, she has a change of heart. Something inside her does not desire to go back into non-existence. She fears the day that Gendo will finally not have a use for her and abandon her. Gendo then appears in front of Rei, saying that today is the day for which Rei was created. He asks her to come with him, and she agrees. The purpose is revealed to be Instrumentality. Rei plays an important part in beginning the process, though the details are mostly left out.
Shinji senses the beginning of Instrumentality, and describes it as feeling "good", like his body is melting away and his sense of himself is expanding ever outwards. It is explained that Instrumentality is the melding of all minds and souls. In order to fill the void left by loss in their hearts, the people of the world will return to nothingness. But Gendo interjects at this point and claims that the latter statement is incorrect; Instrumentality is not a return to nothingness, but a return to the original state in which life existed. Mankind will return to their mother who had been lost to the world and here all souls will be able to find eternal peace. Misato asks if this is the truth behind the Instrumentality Project, which Ritsuko confirms: The reason for the project's creation is to fill a void that exists in every human heart. This void is the source of fear and despair. It is something that humans seek to fill throughout their whole lives and is a wound that they seek to heal through their interactions with others. Misato, however, is not pleased with this explanation. She angrily asks Ritsuko who it was that came up with Instrumentality and set themselves up as the overseers of mankind, calling it a conspiracy to to deceive everyone. Ritsuko retorts that even if she is angry, Misato was nonetheless subconsciously seeking this out.
The focus now shifts to Misato. Shinji appears, conversing with her, and telling her that in order to understand himself better, he is going to have to look deep inside Misato and verify the image of her that exists in his mind. The question is posed thus: What is it that you wish for, Misato? Misato had desired to be a good girl in her childhood. A vision of a young Misato appears and says that because her father is never around, she has to be good for her mother's sake. Her mother always cries, alone, because of her father not being there. Perhaps if she acts that way, her father might not hate her as much and he might come back. But the older Misato hates her father. She is sick and tired of having to keep up the "good girl" charade and want to see her image and reputation completely sullied and ruined. She wants to experience what life is like when she is no longer forcing herself to be "perfect". Ritsuko asks her if that was why she slept with Kaji. Misato denies that, saying that she slept with Kaji because she loved him for accepting who she was in reality.
At this level of awareness, Shinji can also peer into Misato's mind and is presented to a moment from the week her and Kaji spend in bed together during their college days; he watches their fornication unfold with a disgusted sneer on his face. Misato protests, begging for Shinji not to be shown this side of her. Kaji and Misato herself ask why she is upset and point out that she was happy enough to show this side of her without scruples to Kaji. If that is the case, could it be that she wanted to show this side of her to her father? Misato denies that. It was because she saw her father in Kaji that she broke up with him. Kaji tells her that because of that, she shouldn't just punish herself so that she can feel some fleeting sense of justification for her actions. He asks her to stop, and she sarcastically asks whether he'll start telling her to be good from now on. She says that all men are like this. They always seek the easy way out, running from the harsh reality. But then, for the men that have run from her, wouldn't they just be running away from the harsh reality that is her? She acknowledges it. She is filthy. Ritsuko, Ibuki, and Asuka call her out on how dirty and immature she is. On whether or not she is truly happy, Misato thinks that she is, at first. But soon she changes her stance. She acknowledges that she is not happy yet cannot seem to accept that her unhappiness is the reason for her promiscuity and her desire to be with people. While the Misato that everyone sees at work is a successful woman who has reached high ranks and is on top of things, the real Misato is broken and always crying. She only seeks to fill the void in her with pleasure.
The focus now shifts to Asuka, once again. Asuka, as a child, had decided that she was going to live by herself and that she didn't need anyone. Her adamance unsettled her stepmother, who distanced herself from Asuka, only focusing on being her husband's lover. Asuka, however, secretly desired to be with her mother. She didn't want her mother to abandon her. Her mother, having lost her mind through the contact experiment, didn't hear a word. Rejected by her husband, she wanted to die and asked the doll she thought was Asuka to die with her. But Asuka didn't want to die; she refused to be her mother's doll, she could think and live for herself. Eventually her mother took her own life, smiling as she hanged from the ceiling. Asuka hated that smile. She hated having both her mothers and her father run from her. She hated everyone since no one would come to comfort her. Her only choice is to live on her own, but that's hard. It's painful. And she hates it.
Shinji, having been watching everyone pour out their hearts and memories, now comes to the forefront. He asks what is going on and Misato subsequently explains that this is the Instrumentality that his father had worked for. This is also what Shinji wanted, contrary to what Shinji himself believed. He is told that his wish for a destroyed world, a world in which no one was saved was what created this reality. However, this reality is not constant. It is moldable and shapes itself actively according to Shinji's wishes. He wished to isolate the world and create a small haven for himself and thus, everyone is now here, sharing his newfound reality.
- Production Foreshadowing: In somewhat roundabout way. Several shots references events that would first be properly explained in The End of Evangelion, such as Asuka inside Unit-02 at the bottom of the Geofront lake, as well the deaths of Misato and Ritsuko. Of course, these scenes likely were included as leftovers from the originally planned finale, which eventually became EoE.