The episode opens with an emotionally distant Shinji sitting in the cockpit of Unit-01. Ritsuko contacts Shinji over the radio and asks him how he is doing (he answers that he's "getting used to it"), then briefs him on the EVA's technical capabilities and tells him how the EVA is powered: a power cable connects the EVA to its power source, and if the cable disconnects, the EVA has a battery that lasts up to five minutes in minimal usage or as little as one minute in combat. Shinji takes in all the info, then enters a combat training simulation, during which he lines up the targets and shoots them with mechanical disinterest. In the control room, Maya wonders why Shinji agreed to continue as a pilot. "He just obediently goes along with what others say," answers Ritsuko. "That's his secret of success in life."
After Shinji heads out for school the next morning, Misato gets a call from Ritsuko, who asks how Misato's "new boyfriend" is doing. Misato admits she has concerns about Shinji's distant behavior; she's noticed that, despite going to school for two weeks, he doesn't seem to have made any friends and his new phone hasn't rung once. Ritsuko relays the fable of the Hedgehog's Dilemma—"The closer we are to each other, the more we risk hurting the other"—and says Shinji probably has a hard time making friends because he fears that pain. Misato remains hopeful he will learn to open up to others as he grows up.
As Shinji arrives in class, he notices the injured Rei staring out the window; elsewhere in the classroom, another student, Kensuke Aida, is playing with a model plane. He is interrupted by the class representative, Hikari Horaki, who asks him if he got around to giving some papers to his friend, Toji Suzuhara, who hasn't been in class for two weeks. Kensuke says he doesn't know where Toji has been lately, and Hikari wonders if his absence is related to the "giant robot incident." Another student questions the possibly of this, as the official word is that no one was injured, but Kensuke interjects that all the collateral damage makes the idea of such an incident causing no injures—let alone no deaths—an outright impossibility.
As their conversation ends, Toji walks into the classroom, noticing the lack of other students. Kensuke tells Toji that many of the students transferred after the Angel attack, then asks him about his absence, to which Toji replies that his kid sister was injured in the battle, and with his father and grandfather's work hours, he was the only one who could keep her company in the hospital. He vents his anger about the pilot of the giant robot—laying all the blame on said pilot for his sister's injury and the city getting wrecked—so Kensuke points out the new transfer student (Shinji) and how he showed up after the incident, which has led to rumors about his identity.
The school day continues as the class's teacher talks about Second Impact without paying any attention to the bored class. Shinji gets a chat message on his school computer that asks him if he is indeed the EVA pilot; almost as soon as he answers "Yes", the class erupts in surprise and quickly surrounds him, asking him questions about the EVA. Hikari desperately tries to reestablish order while a surprised Shinji tries to manage his new popularity—and after class, Shinji is confronted (and beat up by) a furious Toji. Kensuke explains Toji's situation to Shinji in an apologetic tone, but refuses to intervene in the beating and leaves Shinji on his own after Toji finishes venting his anger.
The roughed-up Shinji is approached by Rei, who tells him NERV has placed an emergency call for them: hovering over the ocean, the next Angel—Shamshel, looking like a cross between a giant horseshoe crab and a squid—approaches the city. The civilian evacuation is completed in short order; Toji and Kensuke end up in a shelter alongside the rest of the class. Kensuke laments how, thanks to government censorship of the news, he won't get to witness the event. Inside NERV HQ, Shinji is placed in Unit-01. He wonders why he bothers piloting, noting Toji's beating from earlier and the absence of his father.
Kensuke talks Toji into sneaking out of the shelter to watch the incoming Angel attack. The duo get out unnoticed, find a hill overlooking the center of the city, and watch as NERV launches Unit-01 against Shamshel. Kensuke is awestruck by the sight and pulls out his camera to film everything; Toji is stunned into silence; and Shinji...is left in a panic after he screws up the initial attack. Shamshel goes on the offensive by using whip-like tentacles to attack Unit-01, so Shinji is forced into retreating while he frantically tries to dodge the Angel's attacks, but he is eventually struck and takes a fall. The EVA's power cable is cut in the process, which leaves Shinji with only battery power. The Angel grabs Unit-01 and tosses it into the air; it lands right next to Toji and Kensuke, only barely avoiding landing on top of them. When Shamshel moves in for another attack, Shinji manages to hold the Angel at bay by grabbing its tentacles, then realizes he can't counterattack without possibly killing Toji and Kensuke. Misato orders Shinji to get Toji and Kensuke inside Unit-01 despite Ritsuko's protests that the duo will disturb Shinji's synchronization with the EVA. Once both boys are aboard, Shinji pulls on the Angel's tentacles and manages to chuck it away. Misato immediately orders him to retreat.
Despite having one minute of battery power left, Shinji stands in place, chanting "I mustn't run away" while Toji begs for a hasty retreat. Shinji decides to go all out against the Angel: he draws the EVA's knife and runs towards Shamshel, screaming in blind anger all the while. The Angel pierces the EVA's abdomen with its tentacles, but Shinji ignores the pain and continues his suicidal charge, eventually plunging his knife into the Angel's core. He keeps screaming as the blade cuts its way into the Angel, refusing to budge until either he or the Angel is destroyed. Shamshel finally dies a second before Unit-01 runs out of power.
When the battle is over, Shinji breaks down crying in front of Kensuke and Toji, who both look silently on in pity—and fear.
Three days later, Kensuke and a moping Toji are hanging out in class. Toji notices how Shinji hasn't shown up for school after the battle; Kensuke asks Toji if he is worried, but Toji tries (unconvincingly) to deny the notion. "Toji, for someone who's so tactless, you're pretty stubborn," says an exasperated Kensuke, who then tells Toji that if he had apologized to Shinji back then, he wouldn't have had to agonize over it for the past few days. Kensuke gives Shinji's phone number to Toji: "If you're so worried, why don't you call him?"
At the school's public phone, Toji starts to dial Shinji's number. He soon decides not to call and walks away.
Tropes:
- Broken Tears: Immediately after the both physically and emotionally challenging battle against Shamshel, a mentally exhausted Shinji is unable to hold himself together and breaks down weeping. Both Kensuke and Toji look on in sympathy.
- Meaningful Background Event: The fact that Japan is eternally stuck in summer is dropped by a background conversation on a radio in episode.
