A desolate Shinji stands at the lakeside where Misato left him the night before. He is dripping wet, as if he has attempted to drown himself. Later, Shinji goes to visit the comatose Asuka in the Geofront's hospital. He begs her to wake up, saying he cannot face either Rei or Misato as both of them scares him. Getting increasingly desperate, he starts shaking her unconscious body more and more violently, and ends up accidentally ripping open her shirt, exposing her breasts in the process. He proceeds to lock the door to the room and masturbates to the sight. Looking at the end result, he despairs at what he has done.
In Central Dogma, Maya, Hyuga, and Aoba are gathered for their night-shift. They wonder why the head quarters are sealed off, and NERV is on alert seeing as Kaworu was the last of the Angels. Aoba theorizes that NERV is probably going to be disbanded, but that still leaves the question about happens to the Evas and the personnel. Hyuga says that they have no other choice than wait until the mysterious "Instrumentally Project" scheduled by the high command commences. Meanwhile, Misato is overlooking the Geofront's lake in her car. She has found out what the intention with the Instrumentally Project is: To end mankind's existence as separate individuals and merge them together to one being. And just like Kaji predicted, SEELE intends to use the Evas for their plan.
SEELE meets with Gendo and Fuyutsuki and delivers their ultimatum. As the Lance of Longinus is out of their reach, they cannot use Lilith for the Instrumentally Project, and therefore needs her offspring, Unit 01, instead, so they can direct the process. Gendo stoutly refuses to surrender the Eva to them, saying that "Death creates nothing." Keel coldly answers: "Then you deserve death!" ending the meeting.
That night Rei leaves her apartment, never to return. In Misato's apartment Shinji lies in his bed and stares out into the air. His SDAT has out of batteries.
Early next morning, Misato is hiding in a server room as she is hacking into the MAGI. As she finally manages to uncover the classified information on Second Impact, the server is suddenly locked, and she thinks she has been discovered. But she quickly concludes that it must be something else.
NERV goes on full alert, as their communication lines are cut off and the MAGI is under attack from its sister units in other countries. Fuyutsuki realizes that SEELE must be behind it and deduces that they are putting all their resources behind it. As Misato heads back to the command center, she learns that NERV has lost its legal status and is ordered to surrender to the Japanese government, she also finds out that Ritsuko as been released from her captivity to help repel the hacking attempt. Ritsuko's efforts are successful, but Misato, Gendo and Fuyutsuki realizes that it was only the first stage of the invasion, and that the next step will be a full-on attack to take the Evas by force.
With their attempt to take the MAGI remotely foiled, SEELE calls for the invasion force to attack. Using their control over the Japanese government, they have convinced the prime minister and his staff that NERV plans to initiate Third Impact, and they have in turn mobilized a large JSSDF detachment against Tokyo-3. Having been given the order, the JSSDF takes out all of NERV's surveillance equipment on the surface. The experienced JSSDF forces then starts entering the Geofront proper and faces little resistance from the NERV personnel, which they indiscriminately slaughter as they come across them. Meanwhile, Misato directs the defense against the invasion. Knowing that the pilots are a priority target, she orders Asuka to be inserted into Unit 02 and hidden on the bottom of the Geofront lake as she will be safer there. Shinji and Rei, however, are nowhere to be found.
Fuyutsuki concludes that Nerv's efforts is ultimately futile and that it is only a matter of time before they are completely overrun. Gendo then leaves, heading for Terminal Dogma, asking Fuyutsuki to see it through. Fuyutsuki, in turn, asks Gendo to give Yui his regards. Meanwhile Shinji is found hiding under a flight of stairs at the border of the front line. Misato orders to seal off most of the complex with Bakelite, as she hands the command over to Hyuga, before she heads out to save Shinji herself. As the bridge bunnies proceed to arm themselves, Hyuga notices that they are ridiculously underequipped to handle a human invasion, and Aboa theorizes that it was probably deliberate, and the end game they are facing now had probably been planned right from the start. Just then, a JSSDF squad breaches Central Dogma, and the personal frantically returns fire. Maya freezes up, refusing to shoot at other people, but Aboa angrily scolds her, telling her that "kill or be killed!" is the only rule now.
Gendo finds Rei meditating naked amongst the remains of the other clones in Terminal Dogma. He tells her that it is time, and while she glares coldly back at him, but she follows him regardless. Meanwhile, Shinji has been found by three JSSDF soldiers, who prepares to execute him. But just in the nick of time, Misato arrives and kills them. She then takes the unwilling Shinji away, knowing that getting him into Unit 01 is their only chance of survival.
Despite heavily casualties, the attack on Central Dogma has been repelled for now. The bridge bunnies wonders why the JSSDF haven't used something heavier on them. Just then, an N2 mine is dropped on top of the Geofront, blowing off the top of the protective dome.
The JSSDF has now captured and secured Unit 01. They have also found Unit 02 on the bottom of lake and decides to bomb it with depth charges. Just then Asuka regains consciousness, and is surprised to find herself in the Eva. But before she can contemplate further, the JSSDF starts their bombing, causing her to panic. While she declares in a mantra that she doesn't want to die, her mother's soul suddenly awakens. Asuka, realizing that her mother was watching over her in the Eva all along, synchs up with Unit 02 and starts inflicting carnage on the JSSDF ranks, who are unable to get through the Evangelion's AT Field. After suffering heavy losses, they manage to cut Unit 02's power cable, but Asuka refuses to let that stop her.
Meanwhile Misato is driving Shinji towards the Eva cage. She explains her findings, that just like the Angels spawned from Adam, mankind spawned from Lilith making them the 18th Angel, meaning that they couldn't coexist with the other Angels. She tells him that their only chance of getting through the day is by holding off the invasion with the Evangelions, as SEELE is sure to use the Mass Produced Evangelions series in the attack sooner or later. Shinji remains unresponsive, until the news of Asukas reawakening reaches Misato. And just then, in their anger about being opposed by Unit 02, SEELE orders the Mass Produced Evas to be unleashed upon the Geofront. Dropping down from specialized airships, eight white Evas, Unit 05 through 13, all controlled by dummy plugs, lands in the Geofront. They waste no time in surrounding Unit 02, but Asuka, despite running on battery power, is confident that she can kill them all.
Reaching the emergency elevator to the Eva cage, Misato and Shinji is suddenly attacked by a JSSDF patrol, and before they can escape, Misato is shot in her torso. The soldiers consider pursuing them for a moment, but as the area is secluded for demolition, they retreat instead. The heavily wounded Misato tells Shinji that he must pilot the Eva if he wants to survive, but he answers that he wants to die, considering himself a horrible person for what he did to Kaworu and Asuka. Misato tells him that he must face what he did and accept it, and that she will never forgive him if he just gives up. She then learns in and kisses him deeply, telling him "That was an adult kiss. We'll do the rest when you get back", before handing him her pendant, pushing him to the elevator, and sending him on his way, she then collapses from her wound. With her last breaths she asks Kaji for forgiveness, wondering if she did the right things. The last thing she sees is a ghostly Rei standing over her. The floor is then blown up, killing her in the process. In the elevator, Shinji wipes his mouth and realizes that he has Misato's blood on him and that she is probably dead. He cries bitterly.
Asuka is fully engaged in a bloody fight with the Eva series, and she wonders where Shinji is. Hearing her over the radio, he has meanwhile found out that the JSSDF has covered Unit 01 in Bakelite, meaning that he cannot get inside it.
In Terminal Dogma Gendo and Rei reaches Lilith's chamber. They are confronted by Ritsuko, who has used the confusion to sneak away. She tells Gendo that she has rigged the MAGI to self-destruct, considering it her ultimate revenge against him. But just as she presses the button to the remote and nothing happens, she finds out that Casper has rejected the command. Gendo points a gun at her and says some last words to her. Bitterly Ritsuko calls him a liar, and is shot by him, causing her to fall into the pool of LCL. Like Misato she sees a ghostly Rei before she dies.
In the fight against the Eva series Asuka seemingly has the upper hand, having maimed several of her opponents. But suddenly one of them throws a copy of the Lance of Longinus at her. It penetrates her AT-Field and hits her Eva in the face, causing Asuka to scream out in pain and panic. Falling over, she also runs out of power, and is helpless as the injured members of the Eva series start regenerating due to their S2 engines and close in on Unit 02. Flocking like vultures, the series attacks the red Eva, ripping it apart. The bridge bunnies and Shinji hears everything over the radio, unable to do anything about it. Finally the Eva series takes to the sky and leaves a heavily mutilated, barely functional Unit 02 behind. Asuka, in massive pain and filled with rage, defiantly reaches out for them, swearing repeatedly that she will kill them all, and manages to force her Eva into berserker mode. But it is all for nothing as the Eva series throws their remaining spears at the Eva, killing both it and its pilot.
Hearing the bridge bunnies panicking about Asuka's death over the radio, a distraught Shinji mumbles that there is nothing more he can do, before Unit 01 suddenly moves on its own, breaking free of the Blakelite. Shinji, knowing it was his mother who moved it, enters the Eva. Gendo senses this, knowing it means that he can carry out his plan.
Unit 01 deploys a massive AT-Field, blowing up the NERV HQ pyramid in the process. The JSSDF command looks on in shock as the Eva hovers out of the wreckage on wings of light, calling it "The devil himself!" Inside the cockpit Shinji quietly calls out for Asuka. Looking towards the sky, he screams in horror as he sees the Eva series carrying off Unit 02's mutilated remains.
- Plot Armor: Hyuga, Aboa, Maya, and Fuyutsuki survives the attack on Central Dogma. What especially makes this example stand out is that 1) literally every single other personal posted there, all of them unnamed Red Shirts, appears to have perished in the attack, judging from the establishing shots, and 2) it happened off-screen so we don't see exactly how they managed to pull through.
- Speak of the Devil: Hyuga wonders why the JSSDF hasn't used N2 mines on them, seconds before they do just that. Aoba then says the trope name as the HQ is rocked by the explosion.
- Where's the Kaboom?: Ritsuko's failed plan to activate the self-destruct through the MAGI. It is not a technical issue that does it, however, but rather a result of Casper, which is based on the womanly aspects of her mother Naoko, choosing her lover over her daughter.