Fade to Scene I: we see Tokyo 3 under attack by the Third Angel. An Evangelion is engaging it. The Eva, the gold Unit 00, is not faring well at all.
Switch to NERV control room: We see Katsuragi Misato, Akagi Ritsuko, and Arisugawa Juri watching the monitors. There is activity around the control room.
Voice Over: Synch-rate is falling!
Misato: What? Miki, what's going on?
Juri to Misato: Get him out of there, Misato-sempai.
Ritsuko to Maya: Is Shinji ready in Unit 01 yet?
Maya to Ritsuko: Not yet! He's not even in the Entry Plug.
Ritsuko looks at Misato, who idly glances at Juri. Juri is idly looking down at her left hand, her right hand twisting a ring around the knuckle of her left ring finger.
Ritsuko to Miki (off): Miki, Shinji is coming. Hold out just a few moments longer.
Switch to the inside of Unit 00's entry plug. We see Kaoru Miki in the pilot's chair, looking pretty ragged.
Miki to Ritsuko (off): Hurry...this thing is taking me apart...
Switch to Tokyo 3. The Third Angel is holding Unit 00's head and blasting it. Unit 00's AT Field is holding, and then gives.
Switch to Unit 00's Entry Plug: We see Miki holding his head, screaming.
Switch to NERV control.
Maya: Unit 00's AT Field has been penetrated!
Misato: That's not possible...
Ritsuko: Synch-rate has fallen ten points, the Eva isn't responding to him.
Juri to Miki (off): Miki-kun! Evacuate!
Misato: Where the hell is Shinji???
Ritsuko: Unit 01 is launching now.
Switch to Unit 01. We see it launching from NERV up to the surface of Tokyo 3. In the distance we see the Third Angel continuing to fire at Unit 00's head.
Switch to Unit 01's Entry Plug: Ikari Shinji is looking in fear at the fight.
Switch to Tokyo 3: Unit 01 races to the fight. We see Unit 01 pressing against the Angel's AT field. The Angel releases Unit 00.
Switch to Unit 01's Entry Plug: Shinji looks fanatical, eyes wide and his arms tense like he is choking the life out of something.
Switch to Tokyo 3: Unit 01 is reaching through the Angel's AT field. As soon as it reaches through, one hand grabs the Angel and the other begins repeatedly pounding it.
Switch to NERV control: Juri holds both hands to her lips, wide-eyed. Ritsuko is standing over Maya. Misato is next to Juri.
Misato: How's Miki?
Maya turns her head slowly to Misato, avoiding Juri's eyes.
Maya to Misato: No life signs from the pilot of Unit 00...
Juri turns to Misato, but she is already moving over to Maya's station.
Misato to Maya: Eject the Entry Plug! Get Miki out of there!
Switch to Tokyo 3: Unit 01 is ripping the Angel apart savagely. We see the mechanisms on Unit 00's back open and reveal the Entry Plug, which is launched out. Unit 01 takes Unit 00's Progressive Knife, and stabs it into the core of the Angel.
Switch to Unit 01's Entry Plug: Shinji is gritting his teeth and looking mad with rage.
Back to Toyko 3: The Angel explodes.
Back to NERV control: All four women look up at the view screen. When the light clears, we see Unit 01 over the dead angel. Unit 00 lies next to it with its head gone. Move across the city to the Entry Plug of Unit 00.
Misato: Rescue the pilot. NOW!
Juri is holding her ring finger, tightly, looking down. We see her Rose Signet briefly as she shakes. Her eyes are closed, head down, and is holding back tears.
Misato to Juri: Juri-san?
Misato walks over to Juri, placing a hand on her shoulder. Juri shrugs it off and looks up towards the upper level of the control room very coldly, then walks out. Misato watches Juri leave, then looks up to the upper level, where we see Mikage Souji standing next to Ikari Gendo. Gendo is looking intently at the control room, the light reflecting off his glasses preventing us from seeing his eyes.
Switch to Tokyo 3: The rescue crews are opening the Unit 00's Entry Plug. We don't see Miki inside, the angle is positioned so we see the crews looking in. We see Miki's hand, bloodied, lying still in the pilot's chair. We also see his Rose Signet.
Crew member one: Oh my god...
Crew member two pulls back in horror, turning away.
Switch to Gendo's conference hall. He is sitting almost exactly as he was. Mikage is standing over him.
Mikage to Gendo: The recovery crews have reached Unit 00's Entry Plug.
Gendo to Mikage: The pilot?
Mikage to Gendo: It is doubtful he will ever pilot Eva again.
Mikage stares intently at Gendo, who is unmoving.
Gendo to Mikage: It is no matter. A back-up will be arriving within the week. We'll rely on Unit 01 until then.
Mikage to Gendo: A back-up?
Gendo to Mikage: Yes.
Switch to Unit 00 within NERV: We see Misato and Ritsuko looking at the wreckage of Unit 00. Repair crews are scattered over it like ants.
Misato to Ritsuko: Have you determined what happened to Miki?
Ritsuko to Misato: He lost. Simple as that.
Misato to Ritsuko: Is it?
Ritsuko to Misato: Yes. He lost his nerve and cracked.
Misato to Ritsuko: Shinji isn't taking this well. Miki was his only friend.
Ritsuko to Misato: You should talk to him.
Misato shakes her head.
Misato to Ritsuko: He won't talk to anyone right now.
Switch to NERV medical ward. We see Miki all bandaged up, with IV's in his arm, unconscious. Shinji is looking at him from behind the protective glass of the room. One of his hands is pressed against the glass. We see Shinji's Rose Signet as well.
Shinji: Wake up, Miki...wake up, Miki...wake up, Miki...
Switch to Shinji's face. He is staring ahead blankly, looking at Miki.
Shinji: Wake up, Miki...wake up, Miki...wake up, Miki...
Classroom at Ohtori Academy: The students are filling into the room, lingering, etc. We see Shinohara Wakaba and Aida Kensuke sitting next to each other amidst everyone else speaking.
Kensuke to Wakaba: Hey, Wakaba-san?
Wakaba to Kensuke: Hmm?
Kensuke to Wakaba: What's up with Kozue?
He nods towards the windows, angle pans over until we see Kaoru Kozue, arms folded on her desk and laying her upon them.
Wakaba (off): Oh, don't you know?
Kensuke (off): Uh-uh. What?
Back to Wakaba and Kensuke.
Wakaba to Kensuke: Oh. Well, her twin brother Miki hasn't been at school, since...well, you know...the day the monster attacked the city. Apparently he got really hurt and nobody knows when he'll be back.
Kensuke to Wakaba: I was wondering why she was acting so odd lately. Come to think of it, I was wondering where that guy was too.
Teacher walks in; class is called to order. Following the teacher in is Tenjou Utena, but we only see her from behind, from her shoulders to her hips.
Teacher: Good morning, class. Today a new student will be joining us.
Utena: Hello, I'm Tenjou Utena.
We see our first look at Utena, a young woman dressed in a male uniform with a black jacket. Kensuke looks impressed.
Kensuke (whispered): Amazing...
Pan to Wakaba, who rolls her eyes at Kensuke, then as she focuses back on Utena.
Wakaba (whispered): She's incredible...
Switch back to Utena, who smiles, and now pulls up her arms and holds her books against her chest. She tilts her head and closes her eyes as she smiles, and as her hands become visible, we see her Rose Signet. In the background, various female and male voices offering quiet praise about the new student. Pan across room. We see the classmates with their respective expressions. All of them, regardless of gender, are in awe of Utena. Stop on Ayanami Rei. Rei gasps as she looks directly at Utena. Then back to Utena again, we see her full stance, then zoom to the Rose Signet. Rei looks intently at the Rose Signet. Rei bites her lip and looks down. Rei does not wear a Rose Signet, but she looks at her hands regardless. Kensuke catches this, we see him raise a curious eyebrow at Rei, then turn back and return to admiring Utena.
Switch to Gendo's conference room. We see Mikage, Gendo, Ritsuko, Misato, and Juri. They are sitting around a table.
Mikage: So, the Angels have returned after 15 years.
Ritsuko: Yes. And we defeated the first of them.
Misato to Ritsuko: But we lost a pilot in the process. Possibly even two. I wouldn't call this a victory yet.
Gendo: Destroying the Angels is our only concern. There will be other pilots.
Juri shoots Gendo a wicked look, but he either doesn't see it or ignores it. Misato doesn't look too happy with the comment either. Mikage does notice Juri's stare, and his own expression softens.
Mikage to Misato: How is Miki?
Misato to Mikage: Still in a coma. The doctor's don't know if he'll ever come out of it. Shinji's been at the hospital every day.
Mikage to Ritsuko: Do you think Shinji will continue to pilot Unit 01?
Ritsuko to Misato: Katsuragi-san?
Misato to Mikage: Maybe. He's pretty shaken up right now. He says he will, but it's too early to know for sure.
Gendo: What is the condition of Unit 00?
Juri continues to stare down Gendo, and Gendo continues to ignore her.
Ritsuko: Head unit was 75% destroyed. Much of the neural interfacing was fried in the backlash from Miki's mind. But repairs have gone well, and Unit 00 should be operational before the end of next week.
Misato to Gendo: But we don't have a pilot for Unit 00.
Mikage to Misato: The latest report from End of the World reveals the identity of the Fourth Children.
Mikage slides a folder across the table. Utena's picture is paper-clipped to the outside. Misato and Ritsuko look at the picture. Juri doesn't look, in fact, she is doing her best to ignore the picture entirely.
Switch to the Ohtori Academy Courtyard. Wakaba, Kensuke, and Utena are walking.
Wakaba to Utena: I'm Wakaba, and this is Aida-kun.
Utena: Pleased to meet you both.
Kensuke to Utena: Hey, Utena-san?
Utena to Kensuke: Hmm?
Kensuke to Utena: Why are you wearing a boy's uniform?
Wakaba begins fuming, looking angrily at Kensuke.
Wakaba to Kensuke: Aida-kun...
Utena sees Wakaba, grins, and chuckles.
Utena to Wakaba: No, no, it's all right, really. I wear this to be a Prince.
Wakaba and Kensuke stop in their tracks.
Wakaba and Kensuke: What?
Utena turns to them and replies calmly as though it is the most rational thing in the world.
Utena: To be a Prince.
Kensuke to Utena: But you're a girl...
Utena to Kensuke: I'm glad you noticed.
Wakaba and Kensuke shrug at each other.
Wakaba to Utena: You mean, like, rescuing princesses and stuff like that?
Utena to Wakaba: Hmm, stuff like that.
Wakaba (quiet) to Kensuke: Hey, Aida-kun, I'd bet you'd like to be Utena's princess, wouldn't you?
Kensuke looks down, blushes deep red, and then gets self-righteous.
Kensuke (loud) to Wakaba: I don't know what you're talking about! Guys can't be princesses!
Utena looks at them curiously, then chuckles. Enter Ritsuko. She walks up to the three of them. Utena's back is turned to her. Wakaba and Kensuke see her approach and quit bickering. The silence and the surprised faces of her two companions causes Utena to turn around.
Ritsuko to Utena: You are Tenjou Utena, correct?
Utena to Ritsuko: Yes...?
Ritsuko to Utena: I'm Dr. Akagi Ritsuko. Please come with me.
Switch to NERV. We are seeing the repair work on Unit 00. Shinji is staring at it numbly. Focus on damaged head. Then back to Shinji's face. Close up on damaged head. Close upon Shinji's face. Back to Shinji looking at Unit 00.
Misato enters. She walks up behind Shinji and places one hand on his shoulder.
Shinji to Misato: Misato-san...will...will Miki be okay?
Misato to Shinji: I don't know.
Misato bends down to look at Shinji directly.
Misato to Shinji: Shinji-kun...what are you thinking?
Shinji to Misato: I don't...I don't know if I can get back in that thing again.
Misato to Shinji: You saved Miki's life, Shinji-kun. You saved the entire city. You should be proud of that.
Flashback: Shinji remembers seeing Unit 00 getting repeatedly shot by the Third Angel. Shinji remembers Miki screaming in pain.
Misato to Shinji: Hmm?
Shinji looks back to Unit 00, then back to Misato.
Shinji to Misato: I know, but...
Misato to Shinji: But?
Shinji looks down, then back at Misato.
Shinji to Misato: Miki's...
Shinji starts to cry, and Misato stands up and holds him.
Switch to Ritsuko and Utena. They are riding the descending train from the surface of Tokyo-3 into the NERV Geo-Front.
Utena has her face against the glass, looking awed.
Utena: Amazing...to think that all of this is under the Ohtori Academy.
Ritsuko: Under the entire city, actually. This is NERV headquarters.
Utena turns back to Ritsuko.
Utena to Ritsuko: NERV?
Ritsuko to Utena: Oh, I'm sorry. Forgive me, Tenjou-san.
Ritsuko pulls out a NERV ID card and handbook and hands it to Utena. Utena looks at it strangely. We see Utena's Rose Signet again as she begins flipping through the NERV manual. Ritsuko sees the Rose Signet, and states intently on it, her expression one of shock. She says nothing about it though, and quickly recovers. Utena doesn't notice any of this. Her face has been hidden behind the book.
Utena to Ritsuko: What's all this?
Ritsuko to Utena: NERV is a specially funded project of the United Nations.
Utena is looking through the manual idly, paying more attention to the view of Geo-Front.
Ritsuko to Utena: We're here to ensure humanity's future. Surely you must have heard about the attack earlier this week.
Utena closes the manual, no longer interested, but still excited by the Geo-Front.
Utena to Ritsuko: Oh that. Yeah.
Ritsuko to Utena: We at NERV stopped the creature attacking Tokyo-3.
Utena becomes a little more excited.
Utena to Ritsuko: Really? That's amazing!
Utena pauses in thought.
Utena to Ritsuko: What does any of this have to do with me?
Ritsuko to Utena: I think it would be easier just to show you, Tenjou-san.
Switch to the NERV Infirmary. We see Arisugawa Juri sitting next to the comatose Kaoru Miki. Several minutes of silence as the views switch between Miki and Juri, with slow, zooming close ups of each. A door opening breaks the mood. Juri's head turns. We see Ayanami Rei in the doorway. Rei and Juri stare at each other wordlessly for several shots. Juri gets up, walks towards the door, and goes past Rei without saying anything. Rei says nothing to her. Rei's eyes watch Juri the entire way out.
Switch the hallway outside the infirmary. We see Juri walking down the hallway. Misato and Shinji are walking towards Miki's room, and Juri is between them.
Shinji to Juri: Oh, Arisugawa-sempai.
Juri continues walking and doesn't acknowledge either Misato or Shinji.
Shinji to Juri: Sempai?
Juri stops in front of them. Misato looks at Juri with a very concerned expression. Juri's expression is hard, emotionless, but just for a second it begins to crack. We see Misato's face again; she looks like she wants to say something. Back to Juri's face. As her emotionless fašade begins to crumble, she continues walking and goes past them.
Misato: (quietly) Juri-san...
Shinji looks up at her, then to Miki's room. He sees Rei standing over Miki.
Switch to inside NERV. Different views of NERV leading to the cooling chambers where the Evangelions are stored. End with Ritsuko and Utena standing before the head of Unit 01. It's hard to read Utena's face. She is amazed at it, but it's not a very excited reaction either.
Utena: This is how you defeated the creature?
Ritsuko: We call it Evangelion. This is Unit 01.
Ritsuko looks at Utena and vice-versa.
Utena to Ritsuko: A big robot?
Ritsuko smiles and shakes her head.
Ritsuko to Utena: No. A multipurpose humanoid artificial lifeform.
Utena to Ritsuko: Oh?
Ritsuko to Utena: Eva cannot operate alone. It needs a human pilot.
Ritsuko looks intently at Utena. Utena looks a bit uneasy.
Utena to Ritsuko: Akagi-san?
Ritsuko to Utena: We'd like you to pilot Unit 00.
Utena looks shocked.
Switch to Juri's room. Juri is sitting a chair, looking at a picture in a frame. Close up on the picture: we see Juri, Miki, and Soryu Asuka Langley. Juri starts crying, and buries her face in her hands.