Despite the fact that she calls him an “arrogant bastard” who expects her to “come when he calls” she still obeys him, though not completely. She slips in a self-destruction program but it is ultimately defeated by her mother’s mistakes, a common theme throughout the series as her mother chooses her lover over her daughter, choosing Gendo over everything else. Despite Ritsuko’s repeated statements that she doesn’t want to be her mother in the end she is led to her downfall by both of their mistakes, and ends up dead for it, just like her mother.
Misato arrives at the command deck and takes control, very decisive even with everything that has been going on in her personal life she is still cool and collected in a time of high stress. She forgets about everything else when the time comes that she needs to be a leader effectively ignoring everything else, pushing it to the back of her mind and bottling it up until the current conflict is done, resulting in her crashing in her personal life and her relationships destroyed because she doesn’t really understand her emotions outside of combat.
The sole computer that remains is Casper, the personification of the lover, as opposed by the mother and scientist. The others are also named for one of the three original wisemen, Balthasar and Melchior. The computers stand as the voice of reason more than any human being, and their destruction or take over is treated as one of the worst possible things, worse than losing any single person. For Ritsuko however it is much worse, it is losing the last thing her mother left to her, and in fact essentially losing her mother again, which is why she is so adamant in defending it even though it means working for someone she hates. As she leaves the bowels of the machine she comments how she will see her mother again, knowing her death is soon at hand.
Soon after there are some beautiful images of the greenery outside of Tokyo, but it is disturbed by armed forces rushing in and destroying near everything, indicating that the end has begun for NERV, and at the hands of humans not the eldritch abominations they were fighting. It is ironic that the last Angel, Kaworu is arguably more human than these military soldiers who are nameless and wear identical uniforms. Kozo comments that their “final enemy is man” as opposed to the spectral incredibly deadly angels, and that is actually who they lose to, fellow humans.
Makato when confronted by the fact that the human soldiers will soon be assaulting them says he wishes that they would acknowledge that they are all humans, and should not be fighting amongst one another. Despite this he is still willing to fight and kill when it comes down to his life or others. The soldiers are then shown mercilessly slaughtering members of the NERV defense force who are almost unaware of what’s happening, and definitely not prepared for any of this kind of violence. This is shown clearly as guards are assassinated or mercilessly destroyed before they have a chance to retaliate.
The control station descends into chaos as the enemy forces begin to invade. Misato shouts orders and is in her element, collected even with all the madness that is going on around. This is the only place she actually feels right, and may actually be enjoying it as her last hurrah, since NERV is soon to be disbanded. She attempts to secure the pilots safety above all else, as the children are the only people capable of operating the Evas, the ultimate weapons. However Rei is missing, Asuka is comatose, and Shinji has lost all hope.
Rei is bathing in LCL, the lifeblood of Lilith. She is naked, but at peace, completely unaware of what is going on around, all the violence and death, merely content with her life. Rei may be some incarnation of Lilith, cloned from part of Yui’s body and created for Gendo’s needs, both sexual and emotional. She was essentially a puppet for him, and created to help him meet with his one true love, Yui. Unfortunately through Shinji’s affections and Asuka’s fiery personality she created a personality of her own, far from Gendo’s original plan, which leads to the Third Impact occurring quite differently from his vision, flawed as it was.
In the next scene Shinji is shown in an extremely vulnerable position, unable to move or do anything due to everything piling up and pushing him past the breaking point, almost for good. The shot of him is followed by every barrier in the headquarters closing representing how Shinji has closed himself off completely from everyone, as his descent into total depression is complete and he believes no one can save him, or help him. Now some of the walls are being destroyed, but not in a productive way, but by extreme violence, as his walls are broken down only through the explosive situation he is in, and even then only partially and in no way permanently.
Gendo has realized that any defence they have is pointless, and that their defeat is “inevitable”. With this he decides that the only solution is the final solution, to use the ultimate weapon to create a new world. As he leaves Kozo says to give his “regards to Yui” as he knows what Gendo intends to do, and agrees with it. He loved Yui but could never show it as she did not return the feeling, and he was her teacher and mentor meaning any relationship would be deeply flawed, not that that stops many relationships in the series, but in this case Kozo knew that nothing good could come of it, though perhaps in his last moments he could allow Gendo and Yui some happiness.
The soldiers are shown to be incredibly efficient as the world burns around them, and they slaughter any and everyone, killing some soldiers who were hiding with no mercy or empathy. To the audience they are dehumanized not only by their actions, but also by their masks covering much of their upper faces, making them essentially mindless drones to the audience, impossible to empathize with even if they were trying to stop the end of the world, though it’s unclear who are the good and the bad guys here, or if there really are either. At this point there are simply the characters that the audience empathizes with, and those that they don’t.