It is business about as usual as they can get in the Katsuragi household; as Asuka is chewing Shinji out for his constant apologizing and passive attitude, Misato tries to calm her down, telling her that is just how Shinji is as a person. This only serves to annoy Asuka, who accuses Misato of being too soft on Shinji and only being in such a good and relaxed mood because she and Kaji has hooked up again. "There's nothing between Kaji and me," protests Misato, before she—as if on cue—is interrupted by Kaji leaving a message on her answering machine in which he invites her out for a drink, effectively puncturing her claim. Asuka is upset by this, and leaves in a huff.
Later that day, the pilots are called in for another sync test. Misato gives Shinji the result; He has surpassed Asuka in synch rate and now sits on the best score. Shinji is greatly surprised and uplifted by that bit of news, while Asuka reacts with barely concealed anger to an indifferent Rei.
Next day, a weird, reflective sphere-shaped apparition appears over Tokyo-3. NERV is completely caught by surprise, and with Gendo and Fuyutsuki out on business, Misato takes command. As the MAGI are hesitant with classifying the apparition as an Angel, the Evas are send out to investigate it. Asuka teases Shinji, telling him that he should take point, as he is now the pilot with the highest sync rate. With the test results still boosting his self-confidence, Shinji uncharacteristically accepts her challenge and volunteers for the position with gusto, much to her and Misato's surprise. Ritsuko is amused and remarks that Shinji's hormones must be kicking in, to which Misato responds that she'll have to give him a stern talking to once the mission is over.
As the Evas close in on the apparition, the tension gets to Shinji and, in a moment of rashness, he fires a shot against it. The sphere disappears in a flash, and a massive black shadow suddenly appears beneath his feet, and he starts sinking into it. The alarm goes off as the MAGI finally declare the apparition to be the Twelfth Angel, Leliel. The shadow starts spreading over Tokyo-3, and sucks in cars, trees, and buildings. Asuka and Rei narrowly escape the same fate, as they climb to safety on some tall buildings, but Shinji continues to sink down, struggling and screaming to Misato for help all the way, until the head of Unit-01 goes under, and his radio goes silent. Misato orders Asuka and Rei to retreat, prompting Rei (much to Asuka's surprise) to protest, stating that Shinji is still in danger. A clearly distressed Misato only responds by repeating the order.
At sunset, Shinji and Unit-01 are still stuck in the shadow. The Eva's power cable was pulled out, but nothing was on the other side. Misato personally leads the search and rescue operation. It is estimated that the battery in Unit-01 can uphold life-support for 16 hours at best. If Shinji is not out by dawn, he will die. While she and Rei wait for further orders, Asuka says that Shinji himself is to blame for the whole situation, claiming that he got what he deserved in aiming for the top. Rei, upset by her comments, calmly asks her if she is only "piloting Eva just for the praise of others", and Asuka angrily retorts that she doesn't need anybody's approval but her own. Misato interrupts the brewing fight, stating that Shinji did indeed break orders, and will be reprimanded accordingly when he comes back.
Meanwhile, inside the shadow, Shinji is attempting to sleep, while waiting for his rescue. He tries seeing if he can get any data about the outside, but the cameras only shows an utterly empty void, and the radar and sonar are unable to pick anything up, leading to him conclude that whatever space he is stuck in must be incredibly large. Looking at his watch, he notes that he has around 4-5 hours worth of power left.
Ritsuko gathers NERV's technicians around her to explain her findings. The Angel is in fact the shadow itself, while the sphere is a kind of three-dimensional shadow. Unit-01 has been sucked into an inverted A.T. Field, and is stuck in a pocket dimension, a so-called "Dirac sea" which can only really be defined by abstract mathematics. Misato concludes that they have to consider the shadow on the ground the true target, to which Asuka gloomily answers that it means they have no way of fighting it with the Evas.
Shinji wakes once again up and discover that the filtration in the entry plug is starting to fail. He notices that a sickening stench of blood starts filling the plug, and in panic he tries manually opening the escape hatch, only to find that it refuses to budge. He desperately calls for help from Misato, Asuka, Rei, Ritsuko, and even Gendo, but to no avail.
Ritsuko reveals her plan to Misato. A fleet of fighter planers will dump all 992 N2 mines in the world into the shadow, while Unit-00 and Unit-02 will be station at its edges and activate their A.T. Fields, hopefully creating enough energy to destroy the Angel and push Unit-01 out of the Sea of Dirac. Misato questions Shinji's safety in all of this, but as Ritsuko pragmatically answers that saving the Eva is the top priority and that Shinji's life is secondary, she loses control of herself and angrily slaps the scientist. Misato demands to know why Unit-01 is so special and why everyone's so desperate to save it and for Ritsuko to tell her just what the hell an Evangelion actually is. Ritsuko tells her that she has been given all the information, but Misato shoots her an angry glare and tells her that she knows she is lying, to which Ritsuko only replies with a pleading "Trust me." She then announces that she is going to relieve Misato from command of the operation for being too emotionally involved. As Ritsuko walks away, Misato notes to herself the many secrets that have been kept from her.
Nearing death, Shinji suddenly awakes again to find himself on a strange train car bathed in ominous orange light. A younger, shadowy version of himself, a spectre created by Leliel, sits opposite to him. Shinji asks who the apparition is, and it answers that it is Shinji Ikari. It says that people are always composed of two selves, that which is seen by others and that which is seen by the person as his or her self-image. The apparition says that Shinji is afraid of the Shinji Ikari in the minds of others. Shinji affirms that he is just afraid of being hurt. He asks the apparition about who is at fault for this.
The apparition tells him that his father is the one to blame. Shinji refuses to accept that, bringing the blame on himself while memories of Asuka accuse him of constantly thinking that hes the one at fault while memories of Misato console him and say that his worthlessness is just something he believes is true.
He relives the memory of Rei slapping him and asking whether he trusts his own father. Shinji thought that he hated his father, but when he received praise from him, he was ecstatic and suddenly became unsure of his true feelings.
The apparition asks if he plans to live the rest of his life regurgitating and redigesting those few moments of happiness even if he knows that such happiness cannot last. Shinji answers that such an act is enough to keep him alive and says that everyone does it. The apparition then says that if he cannot bring about change or believe that he can bring about change to this vicious cycle, he will not be able to live. Shinji says thats okay because theres too much pain and suffering to keep going on in this world anyways. The apparition accuses him of self-deception, saying that he has made himself blind and deaf to those things that cause him pain. Shinji relives the memory of Toji punching him for injuring his sister, of Misato telling him to let go of what other people say, and of his father telling him to leave.
The memories cause Shinji to bend down and cover his ears, confirming the apparitions accusations. The apparition once again tells him that he cant keep living like this. He cant keep living by linking his happy moments together like a rosary. Shinji asks him why and screams out a question of why the apparition cant just leave him alone.
Back in Tokyo-3, according to the calculations, Shinji's life support system should be nearing its end. Ritsuko decides to advance the operation by twelve minutes.
The apparition starts questioning Shinji about his relationship with his father and mentions the public rumors that circulated about Yui's death, namely the accusations that Gendo murdered her. Shinji denies that they were ever true; he distinctly remember that his mother was smiling on the day she died. Shinji hears his father telling him not to run away 10 years ago, alongside Misato's previous words of encouragement, and the dreamscape starts fading away as Shinji meekly mumbles that he doesn't want to be alone anymore. Awakening once again in the cold and dark plug, Shinji realizes that he is a mere few minutes from death as even his suit is starting give out. Exhausted, he quietly accepts his fate and closes his eyes again to wait for the inevitable end, but he suddenly feels someone gently caressing his cheek. He opens his eyes to see a bright light with him in the plug. A ghostly woman embraces him and he realizes that she is his mother. Flashing back to half-forgotten day at a sunny lakeshore, Shinji sees himself as a young happy child holding a red marble up to his mother, whose face is obscured by shadows. "Is this enough? Well, that's good for you," she says.
Meanwhile, Ritsuko is about give the go-ahead when red cracks suddenly tear through the body of the Angel on the ground. The shadow of the Angel starts shaking violently and turns black, before it is pierced through by a fist and red blood sprays out. A roaring Unit-01, moving on its own power, breaks free of the sphere in what best can be described as a gruesome parody of birth, covered in the Angels blood, which now rains down upon the city. Everyone looks on in horror as the Angel dies along with its shadow, while the blood-soaked Eva howls against the sky. A disturbed Misato asks herself what NERV plans to do with the Evas once the Angels are defeated.
Shinji awakens to an open plug and a crying Misato who embraces him. "I just wanted to see them again..." he mumbles, before slipping back into unconsciousness. Asuka asks Misato if she is still planning on scolding him.
After the operation, Gendo and Ritsuko oversee Unit-01 being cleaned of the Angel's blood. She tells him that Misato is growing suspicious. "Let her be for now," he says. Ritsuko tells him that "If Rei or Shinji were to find out the Eva's secrets, they'd never forgive us."
Shinji awakes in the hospital, with Rei sitting on a chair nearby, having watched over him. Seeing that he is conscious she stands up and starts to leave, telling him that he can just rest for now. Shinji tells her that he is feeling fine, to which she responses: "Well, that's good for you." Remembering his mother saying those exact words, Shinji gasps in surprise as he realizes who Rei reminds him of. His gaze follows her out of his room, and as she opens the door, he catches a glimpse of Asuka lurking in the doorway outside his room. Trying her hardest to pretend not to care, she quickly hides. Amused by this, Shinji begins to chuckle heartily, but pauses as he notices that he still smells of blood.
- Aw, Look! They Really Do Love Each Other: Despite all Asuka's verbal ragging on Shinji during the episode, she still shows obvious concern for him, the prime example being at the end of the episode were she tries (and fails) to covertly eavesdrop outside the door to his room in the infirmary.
- A Form You Are Comfortable With/You Cannot Grasp the True Form: The weird internal psycho-analysis Shinji goes through in this episode to is the result of Leliel, perhaps the strangest of all the Angels, seeing how it is essentially a being that runs on otherworldly mathematics, attempting to make contact with his mind. Most notably, the younger version of himself he meets invokes Leliel's image by wearing a striped shirt.
- Never My Fault: Asuka constantly rags on Shinji for rushing into combat with the Angel and getting himself in trouble, when he wouldn't have done that to begin with if she hadn't taunted him into doing it.
- Not So Stoic: Rei is possibly at her most vivid in this episode, being very distraught when Shinji is sucked into the shadow (so much so that it surprises Asuka), acting openly resentful towards Asuka for the way she talks about Shinji's predicament, and gives the Angel's bloody death a genuinely grim look.
- Oh, Crap!: See above: Rei looks at the Eva clearly thinking, "What the hell is this death mobile I'm piloting?" Ritsuko quickly establishes Rei would never forgive them if she found out the Eva's secrets, but this is Left Hanging.
- Asuka is more explicit in her horror at Unit 01's bloody destruction of Leliel. Even Ritsuko, who knows more about the Eva's secrets than the pilots and Misato, is scared of the possibility of what Unit 01 and the other Eva's might do if they ever turned on humans.
- O.O.C. Is Serious Business: Asuka is dumbfounded when Rei vocally expresses concern for Shinji's safety.
- Wham Episode: Though both Episode 14 and 15 had been building up to it, this episode cements the notably darker tone of the latter part of the series. The first angel with psychic attack abilities appears, Shinji's newfound confidence and complacency in his life as a pilot is shaken to its core, the cracks in Asuka's already fragile psychological state starts to become apparent, and Misato starts wondering just how much she is kept in the dark by NERV.
- Wham Line: When Rei makes a Meaningful Echo of Yui's "Well, that's good for you." It is even this In-Universe, as Shinji does a brief Eye Take when he hears it.
- Yank the Dog's Chain: Shinji, as a character, has until this point been on an upwards trajectory; he has by now gotten fully accustomed his life in Tokyo-3, he is starting to get some genuine enjoyment out of his role as a pilot, he has friends who accepts him for who he is, and there is even signs that his relationship with his father might improve. The beginning of this episode sees him gaining another personal triumph as he is now leading in sync score. By the end of the episode though, his experiences inside Leliel has seriously shaken his confidence, and things are only going to get worse from here...