After the events involving Bardiel and the dummy plug, Shinji holds Unit-01 under his control and refuses to exit the entry plug. He accuses Gendo of trying to kill Toji with "my own hands", and demands that his father explains himself. He threatens to destroy NERV Headquarters using the few minutes of power that he has left if his demand is not met, and refuses to be talked out of it. Cold and pragmatic as ever, Gendo does not speak to Shinji, and instead has the pressure of the LCL inside Unit-01's plug raised until Shinji loses consciousness, commenting "We have no time to waste on a petulant child." Shinji is subsequently forcibly extracted from the plug.
Some time later, Ritsuko and Misato survey yesterday's battlefield, which is still littered with pieces of Unit-03, their talk soon turns to the incident with Shinji, and Misato fears for his state of mind. Meanwhile, Asuka and Rei hang around near the hospital wing while Asuka remarks on how Shinji cant talk himself out of this situation. Rei asks her about Shinji's condition, and Asuka answers that Shinji wasn't injured during the extraction, so he is probably safely dreaming away as they speak. "Dreaming?" asks Rei puzzled. "Yeah. Don't tell me you don't dream?" says Asuka, but Rei doesn't answer her.
Toji lies in the bed next to Shinji and when he regains consciousness, wonders why Shinji is lying in the bed adjacent to him. He then falls asleep again.
The scene then shifts to the train car inside Shinjis mind. Toji is there as well, seemingly as a separate entity, standing in the next car over. Studying his surroundings in a daze, Toji is confused to where he is. As he looks towards the other car, he registers that Shinji and Rei are in there, sitting opposite each other and are having a conversation that he is not able to hear. In the other car, Rei asks Shinji why he threatened to destroy NERV. He says its because his father betrayed him. Even though the two of them was finally able to talk to each other, Gendo didnt try to understand his feelings. Rei continues to press him by asking him whether he tried to understand his fathers feelings. Shinji becomes more frustrated, bending down and covering his ears, saying that he tried. Rei tells him that he is just running from reality again. "What's wrong with that?! What's wrong with running away from unpleasantness?!" Shinji shouts back at her.
At this point, Toji wakes up again to finds Hikari sitting by his bedside. She tells him he has been out cold for three days. Toji is about to ask if it means she has been watching over him the whole time, but she quickly nips his question in the bud and frantically explains that she is just visiting as part of her duties as the class representative. "Yeah, I know that," answers Toji with a knowing smile. He apologizes for not being able to eat the lunch that Hikari made and asks her to tell his sister that nothings wrong with him. He also notices that Shinji is no longer in his bed.
After he regained consciousness, Shinji was detained in a cell to await a debriefing in the Commander's office. As he is brought before his father in handcuffs, Gendo tells him that his insubordination and attempted hijacking of Unit-01 constitutes serious offenses, before asking Shinji if he has anything to say in his defense. Shinji just coldly tells him that he doesnt want to pilot an Eva anymore and has resolved to go back to living with his old teacher. Gendo's only response is to tell Shinji that he is just running away again and he is disappointed in him, but Shinji is unmoved by this. "I assume that we'll never meet again," Gendo notices. "Yes, that's my intent," answers Shinji with clear determination in his voice as he calmly walks out of the office. Gendo proceeds to order the deletion of all of Shinjis data and designates Rei as Unit-01s pilot with the dummy plug as backup.
Preparing to leave Tokyo-3, Shinji is back in Misato's apartment. Having finished packing, he lies down on his bed one last time, as the phone starts ringing. He takes the call and it turns out the caller is Kensuke, who has found out about Shinji's resignment, and he demands to know if it is true, but Shinji remains silent. "Why are you running away again?", Kensuke asks, as he admits that he both admired and envied Shinji. "Damn it! Even Toji became an Eva pilot, while I-" he continues, obviously trying to keep his voice from breaking, before he is cut short. A formal voice takes over and tells Shinji that the line is monitored and the call has been terminated for security purposes, thanking him for his cooperation.
At the train station, Shinji has one last conversation with Misato. She tells him that his life will be very difficult if he keeps cutting his ties to people like this, but Shinji answers that it might very well be her philosophy, but he can't live like that. Being straight to the point, Shinji asks her the only question he has; why was Toji chosen? She relays him the information she only recently discovered herself; that all of his classmates are potential pilots. She acknowledges what happened with Toji was a mistake, and that she and everyone else at NERV have been placing a lot of responsibility on Shinjis shoulders since he is a pilot of an Eva Unit. She knows it has been a huge burden but remains steadfast in her belief that the end justifies the means. She tells him that she will be saving his pass-code to Headquarters and keeping his room unchanged. He tells her that wont be necessary and firmly states that he wont pilot an Eva again. Misato is surprised by his tone and wonders if Shinji is truly speaking his mind for once. As Shinji waits for his train to arrive, the alarms begin to wail signalling the arrival of the fourteenth Angel, Zeruel, a huge and bulky, vaguely humanoid creature with a leering skull-like mask for a face.
Zeruels attack is relentless and more destructive than anything NERV has encountered so far. With one strike, it manages to pierce through 18 of the 22 layers of armor that protect the Geofont. Asuka is quickly positioned for battle within the Geofront. Rei, however, is rejected by Unit-01 as she attempts to synchronize. And all attempts to activate the dummy plug is similarly instantly rejected. Gendo begins to tense, wondering whether the unit is defying him. He resolves to send Rei out in Unit-00 which still hasnt fully healed its wounds from the last battle. Rei agrees amidst protests from Misato and says that if she dies, she can be replaced.
Soon enough, Zeruel blasts its way through to the inside of the Geofront with Asuka waiting to challenge it, haughtily declaring that she can easily do this even without Shinji's help. She tries to bring it down with every weapon she has in her arsenal but its all completely ineffective and the Angel calmly advances completely unhindered towards Unit-02 before it pauses and extends two razor-sharp limbs to cut off the Eva's arms. As she screams in pain, Asuka charges toward the Angel in a blind rage, while the creature prepares to attack again. Misato orders the nerve connections to be cut just as Unit-02s head is severed from its body.
Shinji, in the meantime, is sitting in a shelter reminiscing about Asuka telling him how pilots like them never have to go through evacuation drills. His thoughts are soon interrupted as Unit-02s head comes crashing through the shelters roof, crushing and injuring several civilians in the process. As panic erupts around him, he stares at the giant served head in stunned horror.
With its nerve connections cut, Unit-02 is rendered completely immobile. Asuka, while still alive, sits fuming with anger inside the Eva, cursing her own weakness. As the Angel moves forward toward NERV Headquarters, Shinji watches the battle rage on. As he stands outside, he sees Kaji taking care of his watermelons. Kaji asks him what he is doing here and Shinji explains to him his decision to quit being an Eva pilot. When Shinji asks Kaji what he's doing here, Kaji replies that now that the end of the world is near, he just wants to enjoy what little time he has left. Optimally he would have liked to have been in the arms of Misato for this dark occasion, but since that was impossible and gardening is the second best thing he knows, he figured that it is what he is going to do as he dies. He explains that it is said that when an Angel makes contact with Adam (who Kaji believes to be under NERV Headquarters) it will result in the complete eradication of mankind. As they talk, Shinji sees Rei come up with an Nmine cradled in Unit-00's arm. Despite both Misato and Gendo ordering her to stop what she is doing and fall back, she runs toward the Angel, pierces its A.T. Field, and detonates the mine. But it has no effect on the Angel, who emerges unharmed from the explosion, and soon Rei is put down as well. Kaji reminds Shinji that all he can do is care for his watermelons at this point. Shinji, however, has something else. He has an ability that no one else has and with that, Kaji leaves the final decision to Shinji. Gathering all of his resolve, Shinji determinately starts running towards the battlefield...
Zeruel blasts an entrance into the central shaft and prepares to descend. Gendo, meanwhile, stands in the Eva Cage, still fruitlessly trying to get the dummy plug to work, as Shinji arrives and demands to pilot Unit-01. As it is registered that the Angel is heading straight for Central Dogma, Misato orders the command center evacuated, but the Angel breaks through the wall before the personal can manage to escape, and its eyes lights up as it readies its attack, but in the nick of time Shinji arrives in Unit-01 to meet it head on. Wrestling with the Angel, Shinji is able to force it into the EVA cage. In its struggle, Zeruel is able to shoot off the Eva's left arm, but, despite the pain, Shinji is still capable of manhandling the creature onto one of the launch catapults and he launches the EVA and the Angel to the surface of the Geofront, where upon he pins it to the ground. In a moment of genuine bloodlust, he tries to rip the Angel apart, but before he can, his power runs out. The Angel soon gets the upper hand and tosses Unit-01 to the side and blasts its chest open, revealing a core inside that looks just like the one in an Angel. Zeruel begins to pound on the Eva's core with its arms, causing it to slowly crack. Inside, Shinji begs and pleads before screaming and demanding for Unit-01 to move. Suddenly, he is shocked into silence as he hears a heart beat in the darkness...
At that moment, Unit-01 goes berserk.
It grips one of the Angels arms and kicks the creature, ripping off its limb and sending it flying backwards. Unit-01 then integrates the torn limb into its own severed arm and regenerates it. The regenerated limb, however, is nothing like how it looked before and actually looks like a human arm. The Angel tries repelling Unit-01 with its A.T. Field, but with a swat of its hand, the Eva extends its own A.T. Field, which smashes through the Angel's barrier and slashes the creature, making its blood and chunks of its flesh spray all over the Geofront. Ibuki notes that Shinjis sync ratio with Unit-01 has reached an astonishing 400%, with Ritsuko remarking on how the Eva unit is finally aware. As the Angel is down, Unit-01 crawls over on all fours, growling and snarling like an ape. Zeruel, gasping as if it is in pain, meekly attempts to attack the Eva, only to have its face swiftly crushed by Unit-01's hand. The Eva goes on to eat the Angel, with Ritsuko explaining that the Eva has begun assimilating the Angel's Sengine into herself. As the Eva continues to eat, it starts growing, causing the armor to break. This armor turns out to not only protect the EVA but also serve as restraints for the beast inside. "We can no longer stop the Eva," Ritsuko darkly comments.
As Eva Unit-01 stands roaring and howling against the Geofront's dome, Kaji watches it all from a distance. In a combination of horror and grim amusement, he wonders how Ikari is going to explain all of this to SEELE. Inside Gendo's office, Fuyutsuki asks Gendo if this was all part of his plan.
Gendo affirms his suspicions and says that this is only the beginning.
- An Arm and a Leg: It is a bit subtle, but the observant viewer will notice that Toji's right leg is missing in some of the shots during his conversation with Hikari.
- Big Damn Heroes: Shinji arrives in Unit-01 and interrupts Zeruel's attack, just as it is about to point blank blast Misato, Ritsuko, Fuyutsuki, and the bridge bunnies to smithereens.
- Blood Is the New Black: Half of Gendo's face and body is splattered with blood from Unit-01 when it's arm is dismembered during the battle with Zeruel. He still wears said blood on his face when him and Fuyutsuki watches the berserk Unit-01 from his office, lending him quite a lot of menace as he smirks in triumph at the sight and declares that It Has Only Just Begun.
- Call to Agriculture: Kaji once again tends to his melon patch amongst the chaos of Zeruel's attack. In a dark twist on the trope, he does so because he is facing the end of world.
- Disappointed in You: Gendo tries this line with Shinji during his reprimanding of him, but at that point, Shinji is so angry with Gendo that the approach has absolutely no effect on him.
- Dynamic Entry: Unit-01's arrival into Central Dogma's Command Center by bursting through the wall, stopping Zeruel's attack.
- Not Afraid of You Anymore: An unspoken version. After the whole Bardiel incident, Shinji finally decides that his father's approval isn't worth a damn to him any more and shows no fear, reluctance, or skittishness when being confronted by him, only responding to him with ice-cold resentment.
- Pyrrhic Villainy: Gendo's lack of reaction to Shinji refusing to pilot Unit 01 again after forcing Shinji to hurt Toji bites him in the ass hard in this episode when, after believing that Rei can always be used as a replacement for Shinji, Unit 01 rejects both her and the dummy plug, leaving NERV down one Eva.