Cut to title sequence and three minor characters talking about the fallout from the end of the angels and the Evangelion program. There are a few things to note about this scene; first it adds a bit more depth to the people who are not movers and shakers, but essentially grunts doing some of the dirty work. They just want to live and do their jobs, nothing more, but as they find out later it is very much who you work for that determines what you will be forced to do. It also foreshadows Maya’s love for Ritsuko, unrequited like so much in the series. Finally it hints at the instrumentality project, which is explained more fully in the next scene.
We then cut to Misato staring out at a purple sea, contemplating the end of human’s evolutions, and the Instrumentality project, realizing that the Evas are the ones that will cause the end of the world. She mentions how that all of making are “separate entities” foreshadowing Instrumentality when every human becomes one. The tools that humanity had created, and what caused the near extinction of the species are what will cause it to evolve into a new form. The scene also shows her depression over losing Kaji and how he actually knew what was going on unlike just about everyone else in the series.
The next scene is one of many mysterious scenes involving the organization SEELE and Gendo, both master planners though Gendo has direct control over the Evas resulting in his plans coming to fruition while SEELE’s flounder in the water. There is much discussion of evolution and god and death, but in the end the only notable aspect of their rantings is that they effectively refer to the Evas as God, as well as the pinnacle of what mankind has created. In the end the Evangelions have become even more powerful than the nuclear weapons they represent in modern society.
Nuclear weapons can be considered the pinnacle of weapon technology, but the Evas are something very different, they are the pinnacle of science and evolution, transcending the boundaries of humanity and nature to become something beyond both, and they can bring about the end of the world even more so than a nuclear war would. Despite the apocalyptic intentions of both groups Gendo says that “Death creates nothing” because he is still mourning for his wife after all these years. The relationships between Gendo and his wife, as well as Rei, will be examined later because they both drive the series so much, especially the conclusion of this film.
The counsel ends by telling Gendo “you deserve death” which seems like a petty insult but given their plans they actually intend to ascend him essentially, so though he deserves nothing more than nothingness he will get the same as everyone else, though what exactly that is may be unassailable. He responds by saying that we exist because we “have the will to live” a call-back to what Misato said about the final angel, and him “giving up” the will to live, because we as humans have a determined survival instinct, against all odds. He then references Yui, though indirectly, because everything he does is because of his love for her.
The next shot is Rei just waking up, and as she is partially a clone of Yui the parallel is obvious. The shots of the moon seek to represent her as a moon goddess, as she has the soul of the second angel, or the first female human/angel, Lilith. Again gods are brought up, though not in any traditional Christian sense, despite the imagery present throughout the series and the motto of NERV. The gods that humanity has created can be destroyed, though not by humans, but by the things that have evolved beyond them, the Evas. Only Gods can kill Gods essentially.
The final shot in the scene is of Gendo’s destroyed glasses from the first episode, crushed by Rei finally. This shows that she is not simply a puppet, but has developed into a human personality. This only happens once she has lost all of her clones and is the only one left, but it was not a direct physical confrontation that caused her to betray Gendo, but her realization that he is cruel to Shinji, and in fact to just about everyone, betraying Ritsuko and her mother, as well as manipulating the counsel he was supposedly working for and lying to everyone including her. In the end it all comes back to Yui and her initial sacrifice, but that will be detailed later.
Again we see Shinji at essentially the lowest he has been, lying in darkness staring blankly at a wall unable to listen to the music that had been comforting him for the rest of the series, as his player has run out of battery. Shinji at this point has lost his mother figure, lost all confidence in his father, lost his friends almost killing one, lost his purpose in life and finally lost Asuka, instead being left with a broken doll. The one person who he could relate to, who was in a very similar situation, had broken down and given up essentially on life, and with what Misato had said to him he is confused about his feeling for Asuka, considering giving up on her as she has.
Misato has gone off on her own to investigate what is really going on with the Evas and the second impact, but the entire complex has come under attack. She reveals she expected something like it to happen and prepares a firearm for battle. When she does this she kicks over a can of beer, her alcoholism a constant problem for her only exacerbated by the loss of Kaji who had been her sole confidence. It is likely she drove Shinji further away with here drinking as well, increasing their separation. Further scenes expanding upon the invasion are next, showing that first SEELE is attempting to infiltrate the computer system, requiring them to recruit Ritsuko back after she was put in prison for destroying all the Rei clones.
The scene begins with Ritsuko in complete darkness, in complete despair. Gendo requests Ritsuko and she comes along, knowing that her love of him is self-destroying and that he doesn’t want her at all, he was merely using her. She still denies this fact consciously but her overt act of violence against Rei was a demonstration of her subconscious telling her what she will never have, repeating the same mistakes as her mother. Gendo has always manipulated the women in his life, aside from Yui and by extension Rei whom he actually cared for, even displaying open affection for them, something he did with no one else including his son.