Begin with large panning shot. We are seeing Evangelion Unit 03, which is black, in the holding cages of Matsushiro, which looks more cramped and compact than those at Tokyo-3. While the panning shot happens, NERV technicians are announcing status in the background. The shot moves from the ground up to the top.
Tech one: T-minus 90 minutes until Unit 03 activation test.
Tech two: Primary power coupling ready and standing by.
Tech three: Pressure lock on all points secured.
Tech one: All refrigeration systems functionally normally.
End panning shot. Switch angles so that we can see Kozue near the top of cage, looking across the distance at the face of Unit 03. Then focus on the face of Unit 03. Back to Kozue, but closer. Then close up of Unit 03's face. Back to Kozue. She eventually looks a little nervous and then looks away.
Shinji (off): Kozue's the pilot of Unit 03?
Switch scenes: Miki is with Shinji, Kensuke, and Toji. All four of them are leaning on the railing overlooking the Ohtori campus. Miki looks downtrodden. Kensuke looks a little sad.
Kensuke: Oh...I was so hoping that I'd be chosen. How can someone like Kozue-chan get selected and not me?
Miki to Kensuke: We were both selected, initially. Kozue didn't want to pilot after they showed us Unit 01. Something about it frightened her.
Kensuke buries his head in his arms.
Kensuke: Wonderful. Not only am I overlooked, but someone who is scared of Eva gets chosen over me.
Toji to Miki: So, why'd she get picked now?
Miki to Toji: She volunteered. Said she'd do it if I wasn't allowed to again.
Toji to Miki: That's not fair. Why didn't they ask you about it?
Miki: Because I was in a coma at the time. They didn't know that I'd wake up when they agreed.
Toji looks gets the "oops, I shouldn't have asked that," face.
Shinji to Miki: You mean they aren't going to let you pilot again?
Miki to Shinji: I'm on "reserve" status. Reading between the lines, though, I think that's a polite way of saying I had my turn and I blew it.
Switch scenes: Wakaba and Asuka are in fencing gear (without masks) in the Ohtori Fencing Gym. Wakaba looks a little uncomfortable, rather out of her element. They are standing side by side instead of in a dueling position.
Asuka to Wakaba: Hold your epee out like this.
Asuka demonstrates and Wakaba does her best to imitate it.
Asuka to Wakaba: Now, hold your free arm like so.
Again, Asuka demonstrates and Wakaba does her best to imitate. As Asuka speaks, both girls move.
Asuka to Wakaba: Now, forward, forward, back, forward, and lunge!
Wakaba does her best, but having never done this before, is hardly perfect. She turns to Asuka, amused.
Wakaba to Asuka: What does any of this have to do with piloting Eva?
Asuka to Wakaba: That's the same thing I asked when they made me learn how to fence. It took me a while to understand that what we were learning wasn't just dueling with swords, but learning how to think tactically and patiently.
Wakaba to Asuka: So much work!
Asuka to Wakaba: Well, you said you wanted to know what it was like to be one of the pilots.
Wakaba to Asuka: How much of this type of stuff did you have to learn?
Asuka to Wakaba: Don't ask. If we weren't undergoing tests with the Evangelions, we were in here. That's what Aida-kun and all the others that wish they were pilots don't understand. So much of what we do isn't fun.
Wakaba nods thoughtfully.
Wakaba to Asuka: So, did Kozue-chan have to go through all of this, too?
Asuka gets solemn.
Asuka to Wakaba: I'd imagine most of her training has been done recently. Though she probably had some of the basics back when she was first selected.
Wakaba to Asuka: Did she get to duel with all of you as well?
Asuka realizes that Wakaba has just quite innocently made an important discovery. Asuka's face shows the surprise.
Wakaba to Asuka: What?
Asuka to Wakaba: No...no, she hasn't dueled with us yet.
Asuka takes Wakaba's epee and begins shooing her out.
Asuka to Wakaba: Finished just in time for you to go meet your boyfriend.
Wakaba to Asuka: Oh...thank you, Asuka-san!
Switch scenes: Utena eating lunch with Rei on the Ohtori hillside. Rei eats quietly, seemingly oblivious to everything else. Utena is eating, but she is paying attention to Rei as she does. As Utena begins to focus on her food, Rei speaks to her.
Rei to Utena: What are you thinking?
Utena to Rei: Hmm?
Rei to Utena: You've been staring at me, Tenjou-sama. What are you thinking about?
Utena to Rei: Well...I guess...I was wondering if Miki was right. About you wanting to be the Rose Bride.
Rei to Utena: What about it?
Utena to Rei: I was wondering if you like being the Rose Bride. It must be lonely. Being willing to belong to whoever wins some silly duel. Before all of this craziness started, I thought you must have been longing for friends. I thought you were lonely, and that I could help you.
Rei looks at Utena hesitantly.
Rei to Utena: I...maybe I am lonely.
Utena looks a little surprised by this admission.
Rei to Utena: I...am lonely.
Utena tries to be encouraging.
Utena to Rei: You can have friends, Ayanami! I know you can. Open your heart and talk to people.
Rei to Utena: I'm sorry...I don't know how to feel around others.
Utena to Rei: I'll help you.
Rei looks at Utena uneasily. Utena smiles warmly. Rei relaxes a little bit.
Switch scenes: Back at Matsushiro. Ritsuko and Misato are making last minute preparations. They are in the control room of the complex, looking at Unit 03. NERV technicians are monitoring various stations.
Ritsuko to Misato: You look worried.
Misato to Ritsuko: I'm worried for Kozue. She was so opposed to doing this before. I hope she doesn't think of this as some kind of nightmare she's just willing to endure for Miki's sake. I'm honestly surprised you allowed her to do it.
Ritsuko to Misato: At the time, she was the most promising candidate. She'd already been approved by End of the World. I'm hardly going to reject an approved volunteer when we had no better options.
Misato to Ritsuko: And you, you're not worried that Kozue's fear might prevent her from synching with Unit 03?
Ritsuko to Misato: Shinji didn't want to pilot Unit 01 initially, either, but he was able to synch with it. I think Kozue will be able to adapt.
Misato to Ritsuko: Maybe. I just don't want what happened to Miki happening to Kozue.
Ritsuko to Misato: Nor I. Think positively, Major. When this Eva is delivered, it will be under your command.
Misato: Exclusive possession of four Evangelions.
Misato to Ritsuko: If we wanted, we could bring about the end of the world.
The double connotation to Misato's wording isn't lost on Ritsuko. Her eyes widen a little bit.
Switch scenes: Miki is sitting alone at the piano in the music hall. He's looking at his stopwatch in his right hand. It's now been running for several minutes on end without him stopping it. He relaxes his arm, and stares at the piano.
Begin Sunlit Garden II flashback.
Black screen: 2013.
A younger Kozue and Miki are being taken through NERV by Ritsuko and Mikage. We get the sense that these are two children in a very grown up world, and they aren't entirely certain how to feel about where they are. Signs on doors seem very important and imposing, and everyone in the hallways is much taller than they are. Kozue's hand reaches for Miki's, and they walk through NERV hand in hand.
Switch locations: the young twins are being led into the cooling chambers. They aren't inside the Eva area just yet.
Ritsuko to twins: This is where the Evangelions are housed.
Kozue: And...it's only a giant robot, isn't it? Like in all the anime?
Mikage to Kozue: No, Evangelion is much more than a mere robot. But if it helps you to think of Eva like that, then it's not a poor comparison.
Miki to Mikage: How do you mean much more?
Ritsuko: A robot is simply a machine that requires the use of mechanics to move. Evangelion will respond to your thoughts and reflexes.
Mikage to Miki: Evangelion becomes a living part of you while you pilot it.
They are now inside the cooling chambers. The lights are off, and Mikage leads them with a flashlight.
The lights come on, and the four are standing in front of Unit 01's head. Miki looks at it curiously. Kozue just stares it. Even though the eye lights are off, it seems like it stares back at her. Cut to Unit 01, then to Kozue, then back to Unit 01, then back to Kozue. This scene is reminiscent of how this episode opened. Kozue eventually looks away, then runs out of the room in terror.
He runs after her, leaving Ritsuko and Mikage behind. As he runs through NERV looking for her, the twins pass a younger Juri and a younger Asuka, who both watch curiously together as the twins fly past them one after another. Asuka shrugs. When Kozue can't run anymore, she curls up into a little ball in a corner.
Miki (off): Kozue!
Miki eventually finds her.
Kozue: I can't do it! I can't do it! It's a monster! A monster!
Miki: It's just a big machine.
Kozue to Miki: No! You don't understand. There's something that isn't right about it! I can't, I won't get inside that thing!
Miki to Kozue: It's alright, Kozue-chan. I'll be here with you the whole time. We'll do this together.
Kozue to Miki: No! I don't care! I'm not going anywhere near that monster again! Promise me you won't do this, Miki-chan. Promise me!
Miki looks at Kozue, very disappointed.
Miki to Kozue: It's important that we do this, Kozue. I have to do it.
Kozue to Miki: Miki, no...Miki you don't have to-
Miki has turned his back and is walking back down the corridor.
Kozue to Miki: Miki! Miki, wait, please!
Briefly fade back to Miki in the present, still watching his stopwatch tick by. Then fade into another portion of Miki's flashback.
Miki and Shinji are practicing fencing together. This is done in slow motion, set to the music of The Sunlit Garden. They look very happy; two boys on top of the world, one of those moments that adults long to return to.
Miki (off): We'll get through this together, won't we Shinji?
Shinji (off): Yes. Whatever happens, we'll always be there for each other.
Continue showing them fence for a few seconds, then NERV sirens take over where the Sunlit Garden was playing. The setting changes, and Miki is alone in the Plug Suit for Unit 00. Misato is escorting him to the Entry Plug.
Miki to Misato: Where is Shinji?
Misato to Miki: His Entry Plug wasn't prepared yet, Kaoru-kun. We're getting him ready now. He'll be joining you shortly.
Miki to Misato: Shouldn't we wait for him?
Misato to Miki: There's no time! The Angel is here in Tokyo-3. You have to do this alone until we get Unit 01 up there with you.
Miki to Misato: Alone?
Misato to Miki: This is what you were trained for, Miki-kun! You can do it!
They are at the Entry Plug. Miki hesitates, very much like Kozue several years back at the piano recital. He steels himself, and gets inside. Setting switches and Miki is now in combat with the Third Angel. Unit 00 is being battered about.
NERV tech (off): Synch-rate is falling!
Misato (off): What? Miki, what's going on?
Miki is remembering the incident with Kozue and the piano. It plays over the image of him in the Entry Plug. Then, the image of him and Shinji fencing together happily plays over him.
Juri (off) Get him out of there, Misato-sempai!
Miki (whispers): Shinji...where are you...?
Ritsuko (off) to Miki: Miki, Shinji is coming. Hold out just a few moments longer.
Miki to Ritsuko (off): Hurry, this thing is taking me apart!
The Third Angel grabs Unit 00's head and begins blasting it. Miki screams and screams.
End Sunlit Garden II flashback.
Back in the present, Miki stops the watch, and lays his head down on the piano.
Switch scenes: On the Ohtori campus, Juri is sitting alone. She is fingering her locket, deep in thought. Asuka is approaching her, and sees the locket Juri is holding between her fingers. She tilts her head curiously and walks closer.
Asuka to Juri: Juri-san?
Juri turns her head and sees Asuka. She lets the locket fall back into her clothing.
Juri to Asuka: Yes?
Asuka is distracted by this, but snaps out of it.
Asuka to Juri: Um...I was thinking. Kozue was selected as the pilot of Unit 03, but she hasn't had any training as a duelist. What do you think that means?
Juri to Asuka: Probably that she will start working with us after the boot test in Matsushiro.
Asuka to Juri: But they've known she was going to pilot since I took her to see Miki. How come she hasn't been training with us all along?
Juri tilts her head. Asuka has a good point.
Switch scenes: Back in the control room of Matsushiro. The booting test is starting.
NERV tech: Entry Plug secured within Unit 03.
Ritsuko: Begin Phase I connection.
NERV tech two: Transmitting pulses now. Graph display is within norms.
NERV tech one: Clear through 1-3-5-0.
Ritsuko: Begin Phase II connection.
NERV tech two: Roger. Full nerve link is established.
NERV tech one: Clear through 2-5-5-0.
NERV tech two: Harmonics normal. Absolute threshold approaching. Wait...there's a huge power surge from inside the Unit...
Ritsuko: Terminate the test!
NERV tech one: It's not responding! High-energy response from within Unit 03!
Unit 03's eyes go red. It screams as it comes alive. A bright flash of light is enveloping everything.
Ritsuko: No! Can it be...an Angel?
Everything goes white.
The pilots of the three Evas are all in their respective Entry Plugs now. Brief panning shot of each Eva in its respective position. The Evas have been deployed outside and are awaiting...something.
Utena: An accident at Matsushiro?
Asuka to Utena: Where they were doing the boot test for Unit 03!
Utena is surprised.
Utena to Asuka: There's a Unit 03?
Asuka to Utena: God, Tenjou-san, do you ignore everything that doesn't have to do with Ayanami?
Switch to Gendo and Mikage in NERV control.
Gendo to pilots (off): Enough.
The pilots all snap to attention.
Gendo to pilots (off): Class one combat alert.
Pilots (off): Yes, sir.
Mikage to pilots: There is unidentified movement at the Matsushiro site. Prepare to intercept as it approaches.
Pilots (off): Yes, sir.
Mikage to Shigeru: Send in the rescue team and 3rd Corp. Take care of everything before the JSSDF arrives.
Shigeru to Mikage: Understood.
Shinji (off) to Mikage: What about Misato?
Mikage to Shinji (off): Still no contact from the Matsushiro team.
Hyuga: We've got visual from Nobeyama!
On the NERV display, we see Unit 03 walking towards the direction of the other Evas. A murmur of shock and surprise fills the room.
Mikage: Just as we feared...
Gendo to Maya: Force eject the Entry Plug.
Maya to Gendo: It's not recognizing the termination signal or the ejection code.
Gendo: And the pilot?
Hyuga to Gendo: We have her respiration and pulse, but-
Gendo: From this moment on, Evangelion Unit 03 is abandoned. Recognize the target as the Thirteenth Angel.
Gendo: Develop a front at Nobeyama, as planned, and destroy the target.
Switch to the Eva pilots: They see Unit 03 approaching. The Evas' targeting computers list the Eva as the 13th Angel.
Utena: That is not an Angel.
Asuka: It's Unit 03...
Gendo (off) to pilots: Stand ready for ground battle. Destroy the target.
Asuka looks at the image of Gendo on her monitors.
Asuka: Destroy Unit 03...?
Asuka looks at the approaching Unit 03. Asuka looks down, and then makes what might be the most important decision of her life.
Asuka (screaming): KOZUE!
Unit 02 tears out of its position to engage Unit 03, running to meet it. It drops its Progressive Katana as it runs.
Back in NERV control.
Shigeru: Unit 02 is rushing to engage the target.
Back at the battle. Utena is momentarily stunned.
Utena: Kozue's the pilot?
Utena then steels herself.
Unit 00 leaves its position and begins tearing off after Unit 02. It leaves its Progressive Katana behind as well.
Back in NERV control.
Shigeru: Unit 00 now moving to engage the target.
Hyuga: Both Evangelion Units have abandoned their Progressive Katanas.
Gendo to pilots (off): Tenjou! Soryu! Don't leave your positions!
Back at the battle: Unit 02 is furiously tearing towards Unit 03. Asuka is screaming like an Amazon. Unit 02 leaps over Unit 03, landing feet first squarely on Unit 03's back. Unit 03 falls to the ground. Unit 02 immediately is upon it, trying to rip off the plate of armor that protects the Entry Plug. Unable to rip it out by hand alone, Asuka commands the plating to open and reveal the Prog' Knife. As Unit 02 reaches for the Prog' Knife, Unit 03 rears back and throws Unit 02 off.
Back in NERV.
Hyuga: What are they doing?
Maya: It looks like she's trying to get to the Entry Plug.
Mikage: Trying to rescue the pilot.
Shinji is now moving Unit 01 to join the others.
Mikage to Shinji (off): Ikari-kun, wait!
Shinji stops. Unit 01 doesn't run just yet.
Shinji (off) to Mikage: What are you talking about? We have to rescue Kozue!
Mikage to Shinji (off): Let Soryu and Tenjou attempt that, Ikari-kun. If they fail, though, someone has to stop the Angel.
Shinji considers those words.
Shinji to Mikage (off): You mean kill Kozue.
Gendo to Shinji (off): We mean stop the Angel.
Mikage to Shinji (off): That is an Angel, Ikari-kun. Make no mistake about it. If Tenjou and Soryu cannot get Kozue free, it must be destroyed.
Shinji hesitates, and holds back.
Back in the battle: Unit 00 is upon Unit 03 now. Unit 03 moves too quickly, though, and catches Unit 00 by the neck by extending its arms. Unit 00 is being strangled and doesn't have the reach to attack Unit 03. Utena is gasping for air.
Back at NERV control.
Gendo: This is useless.
Gendo (to pilots): You cannot defeat the Angel this way. Destroy it!
Asuka is getting ready to spring at Unit 03 from behind with the Progressive Knife, but Unit 03 lets go of Unit 00 with one hand (holding it with the other), and turns, catching Unit 02 with the free hand. It now has both Units 00 and 02 and is choking the life out of the pilots.
Unit 01 is aiming the rifle at the center of Unit 03. Shinji is hesitating.
Gendo to Shinji (off): Fire, Shinji! That's an Angel!
Shinji to Gendo (off): I...I can't! Kozue is inside it! I can't kill her!
Unit 01 drops the rifle and charges into battle.
Gendo: Damn it!
Back at the battle: Unit 03 swings around, using Unit 00 as a weight to pummel the oncoming Unit 01. Unit 01 flies backward, smashing into the ground. Unit 03 swings around again, this time smashing Unit 02 into the fallen Unit 01.
Utena and Asuka are fading quickly. Unit 03 simply has too much reach for them, they are losing air, and they won't attack Unit 03 directly for fear of hurting Kozue. Shinji is unfocused as the shock of the blows hit him.
Back in NERV.
Mikage to Hyuga: Cut the synchronization to 60% on Units 00 and 02.
Gendo: Belay that. Cut the synchronization completely to all Units.
Maya to Gendo: Completely?
Gendo to Maya: Yes. Switch to the Dummy system.
Maya to Gendo: But...there are still problems with the Dummy System. And without Dr. Akagi-
Gendo to Maya: It will be more effective than the current pilots. Do it now, Lieutenant.
Maya to Gendo: Yes...sir.
When the synch is cut Asuka and Utena can breathe again. The Entry Plugs go dark. Something behind them starts humming. All three pilots look behind them as the Dummy system goes online.
Unit 02's four eyes suddenly go red. Unit 00's one large eye goes red. Unit 01's two eyes go red.
Back in NERV.
Maya: All systems switched to Dummy plugs.
Shigeru: 48% of the emotional factor is still unclear. Impossible to monitor.
Gendo: It doesn't matter. Release the system. Attack.
Back in the battle, the three Evangelion Units suddenly come alive with horrifying unison and precision. Units 02 and 00 reach up and snap the arms holding them. Unit 03 screams. Unit 01 springs from off the ground and tackles into Unit 03. It falls the ground, the arms being held by Units 00 and 02 rip away as the force of the impact breaks them. Eva blood flies everywhere.
Back in NERV, everyone is terrified as the Evas begin behaving like a flock of raptors, descending upon the fallen Unit 03 in unison and tearing it apart piece by piece.
Utena (off): No! Stop this! Stop it!
Asuka (off): Kozue! No, she'll die! Stop it now!
Maya: Is this the power of the Dummy plug?
Shinji (off): Father, stop this! Please! Kozue!
Gendo looks only too pleased at the success of the Dummy system.
Eventually, there is nothing left of Unit 03 except blood and scrap scattered everywhere.
Shigeru: Unit 03...I mean...the target...is silent.
Switch scenes: Ariel shots of what's left on the battlefield, which isn't much. Scraps of Unit 03 lay everywhere, including the severed arms. Eva blood is omnipresent, and it runs down the landscape into the river, coloring it red.
Switch scenes back to Matsushiro. Rescue workers are everywhere. Misato comes to. Her head and arm are bandaged. We hear the rescue and recovery workers as they speak.
Recovery team: Another survivor over here.
She turns her head. Kaji is next to her.
Misato to Kaji: Ritsuko?
Recovery team: Send this back to 2nd Division, top priority.
Kaji to Misato: Don't worry, she's in better shape than you are. You were very lucky, Katsuragi.
Misato to Kaji: What about...what about Unit 03?
Recovery team: Need three pints of A Positive over here.
Kaji to Misato: Destroyed as an Angel by all three remaining Eva Units.
Misato to Kaji: And...the pilots?
Switch scenes: All three Eva pilots are in Gendo's office. They are still in their plug suits. None of them look particularly happy. Neither does Gendo. All of them stare wordlessly at each other.
Gendo: Disobeying orders. Reckless, childish behavior. Your actions nearly cost us all three Evangelion Units. What have you to say for yourselves?
Utena speaks up first.
Utena to Gendo: You're a heartless, cruel, and evil man.
Gendo is unmoved.
Gendo to Utena: I see. Is that all?
Utena to Gendo: No. I quit.
Utena walks out.
Shinji to Gendo: I never thought you were this much of a bastard.
Gendo to Shinji: Is that so?
Shinji to Gendo: Maybe the rumors were true, and you knew Mom would die and you went through with the experiment anyway. I can't stand to be around you any longer. I refuse to work with such a monster.
Shinji walks out.
Gendo looks at Asuka, who looks down, but says nothing.
Switch scenes: Miki is in the Music Hall, softly playing "The Sunlit Garden" on the piano. The sun is going down. Juri walks in, by her expression she's obviously heard the news about Kozue. Miki continues to play until he notices that Juri is there. He is about to say hi when he sees her expression, and everything in the room goes still. Miki's eyes begin welling up with tears. He clenches them shut, looking like he's about ready to scream but doesn't.
Switch scenes: Miki and Juri are walking through the NERV infirmary. "The Sunlit Garden" plays in the background.
Misato (off): And...Kozue?
Brief clip of the rescue team at the site of Unit 03's demise. They open the Entry Plug and see what's happened to the pilot. This scene is almost exactly like when they recovered Miki in Episode I, down to the still hand with Rose Signet, but there's much more blood.
Miki and Juri stop outside a room. We see only their upper bodies through the windows. Focus out and then focus in on the same hand, without the ring, bandaged and in a cast, elevated from a harness.
Misato (off): Kaji...?
We see the door open and Miki and Juri enter. Juri has one hand on Miki's shoulder.
Kaji (off): The Rescue Team was able to pull her out of the Entry Plug alive.
We don't see all of Kozue. We don't really have to. Judging by Miki's face, and the sheer amount of bandaging visible and all the harnesses supporting her, we probably don't want to. Kozue's injuries are about twice as bad as the ones Miki suffered.
Miki kneels next to Kozue's bed and starts crying uncontrollably.
Kaji (off): But it might be better if she hadn't made it.
Fade to black, "The Sunlit Garden" playing on for a few moments, then silently ending.