Begin with flashback of episode 4. Juri, Ritsuko, and Misato are in the control room watching Utena in the Entry Plug of Unit 01 as it fills up with LCL.
Utena (off): Well, that wasn't much fun. Will I have to go through this every time I sit in this chair?
Juri: Heh. It's twice as much fun on the way back up, Utena-san.
Utena (off): Is that the voice of experience, Juri-san?
Juri's expression goes blank as she looks away from the monitor. Fade to a younger Juri, wearing a white Plug Suit and sitting in the Entry Plug of an Eva, we don't know which. LCL is filling the plug. This is the first time we've seen Juri without any anger beneath the surface; she can only be described as serene. Juri is very calm as the LCL begins covering her. As it reaches her eyes, they close slowly and peacefully. Return to Juri in the control room.
Juri forces a smile to her face and looks back at the Utena monitor.
Juri: You're not the first pilot I've worked with.
Switch to current day. Juri is at the Ohtori Academy, leaning on the railing that overlooks the entrance to the school grounds. In the distance, we can see the still form of the crashed Fifth Angel among the buildings of Tokyo-3. She is alone when it starts, but soon another individual walks up behind her. He is dressed in a student council uniform, but since Juri is leaning on the railing, we don't see his face yet.
Saionji Kyoichi: Well, the Captain of the Fencing Team decides to grace us with her presence.
Juri (looking ahead): Ex-captain. You know I haven't had the time to lead the team in months, Mr. Captain of the Kendo Team.
Saionji (sarcastic): The Student Council has certainly missed your charming personality at our weekly meetings.
Juri turns to him, we now see Saionji fully.
Juri to Saionji: Is there something you needed, Saionji?
Saionji to Juri: The president is concerned that your absences are decreasing the council's effectiveness.
Juri to Saionji: Touga doesn't care one way or the other if I'm there or not. Even if he did, the Vice-Chairman is aware of my activities and has approved my absences.
Saionji to Juri: Ah, you mean the work you do for NERV. One has to wonder what exactly what purpose you serve for them.
Juri to Saionji: What is that supposed to mean?
Saionji shrugs innocently.
Saionji: Well, as everyone now knows, the pilots of the NERV machines are Ikari Shinji and Tenjou Utena. And if you're not a pilot, it is certainly a mystery that NERV could use a fifteen-year old woman in any other capacity.
He shrugs again, very haughty and sure of himself, walking off.
Saionji (leaving): One has to wonder at just how necessary you are.
Juri turns back to the railing, watching Utena and Shinji speaking with each other in the courtyard below.
Juri (thought): How necessary indeed...
Black Screen: 2013
Mikage (off): Arisugawa Juri.
Picture resumes with a file folder being held by Ritsuko. It is identical to the one we saw Mikage hand to her in the first episode, with a younger Juri's photo clipped to the outside. Ritsuko begins flipping through it.
Mikage to Ritsuko: End of the World has identified her as a pilot for the Eva project. Intelligent, determined, fences at the national level and is involved in numerous other athletics as well.
Ritsuko to Mikage: Has she already been contacted?
Mikage to Ritsuko: Yes. She attends school at the Ohtori Academy, so it wasn't hard to locate her and query her. She's extremely interested.
Switch to the Ohtori fencing gym. We see the younger Juri in fencing gear, along with the younger Miki and Asuka there in dueling gear as well. Mikage, Ritsuko, and Gendo are there. Ritsuko speaks as we pan, one by one, over the three children.
Ritsuko (off): Eva is unlike any machine mankind has ever piloted before. It is not simply a matter of mastering controls or simulators. Your will and your reflexes become the will and the reflexes of the Eva. Your mind and your body must be in harmony. In perfect synch. To achieve this, you will learn to think as a duelist must, to anticipate attacks and know how to parry them, to patiently watch for the moment to strike, and to choose your opportunities wisely.
Miki looks intrigued. Asuka looks bored. Juri is in her element.
Mikage: We will not be putting just anyone into Eva, as you already know. What you learn in this room is vitally important to not only your own safety but for that of all humanity. Don't forget that as you practice.
All three: Yes, sir.
Gendo and Ritsuko leave. Mikage remains. A new individual walks in, Tsuchiya Ruka, also in fencing gear. He is a few years older than the pilots, likely in the sophomore year of high school.
Mikage: This is your instructor, Tsuchiya Ruka.
Scene of Miki practicing with Ruka and Juri practicing with Asuka. Mikage is watching from a distant corner. Miki is a good student, and is doing alright, but Ruka's skill is all too clear. Asuka is doing much better against Juri, though Juri still has the upper hand. Ruka defeats Miki, and the two of them stop and watch Juri and Asuka. Asuka, surprisingly, scores a winning touché. Ruka loooks unhappy with this. Asuka and Juri pull off their masks.
Asuka: I won!
Juri to Asuka: Yes, it looks like you did.
Asuka to Juri: Aren't you supposed to be some kind of wonder girl at this?
Ruka: Do it again, please.
Juri and Asuka put their masks back on.
Ruka to Juri: This time, don't hold back, Juri.
Juri looks at Ruka a moment, then nods.
Miki: She was holding back?
Juri and Asuka spar again. A quick battle, ending when Juri scores a solid hit. Asuka pulls off her mask and looks indignant.
Asuka to Juri: Don't treat me like some underling. You don't need to coddle me.
Switch to Juri and Asuka walking together on the Ohtori Academy grounds.
Asuka to Juri: I will beat you some day. It's only a matter of time.
Juri to Asuka: You think so?
Asuka nods confidently.
Asuka to Juri: I can overcome any challenge. You're just a tougher one than I'm used to.
Juri to Asuka: I look forward to the day when you feel you can do it.
Asuka to Juri: Oh?
Juri nods confidently.
Juri to Asuka: Because on that day, I won't hold back at all.
Asuka to Juri: We'll see about that.
Juri to Asuka: You'd best hope for a miracle then, Asuka-san. You asked me not to coddle, so I absolutely won't let up on you.
Asuka smirks at what she sees as her new rival.
Asuka to Juri: I don't need to hope, Juri-san. If a miracle is what it takes, I will make my own miracle.
Switch back to present day, back to Juri leaning on the railing overlooking the courtyard. Her phone rings and she answers it.
Misato (off): Juri-san. Don't forget we'll be leaving tomorrow at 09:00 to meet the Third Branch transport. I need your help preparing for the trip.
She closes her phone and walks off. Cut to a brief clip of Saionji in the background watching her.
Switch to NERV. Utena and Shinji are undergoing synch tests. Ritsuko and Mikage are observing it along with Maya.
Maya to Ritsuko: Tenjou-san's synch rate is five points above the last test.
Ritsuko: But nowhere near what she managed in combat against the Fifth Angel.
Mikage: Do you think that's due to being in combat?
Ritsuko to Mikage: Presumably. She exceeded even Shinji's highest rating when Unit 00's AT-Field developed.
Maya to Ritsuko: And what Asuka has done while Unit 02 underwent tests in Germany.
Mikage: We'll just have to see what happens when Asuka gets here with Unit 02.
Maya looks at the monitors, and then looks a little surprised.
Maya to Ritsuko: Sempai, Shinji's synch rate is up sixteen points.
Ritsuko to Maya: What? Really?
Ritsuko moves in to get a better look.
Ritsuko: Sixteen points? What could have caused that?
We see Shinji's face on the monitor. He looks more at peace than during earlier synch tests.
Maya to Ritsuko: Defeating the Fifth Angel, maybe?
Ritsuko to Maya: He didn't show that type of increase after the other two attacks. Something's changed.
Scene of a United Nations' jet flying high over the earth. Inside, Gendo is sitting alone.
UN Rep (off): May I sit here?
Inside, we see a well-dressed man take a seat neat to Gendo. The plane is empty aside from those two.
UN Rep: The draft amendment to the budget has been passed. And there's more good news. All member nations have approved the construction budget for Unit 06. That is, except the United States, and it's only a matter of time before they approve it.
Gendo: The committee values their own lives above all else. They'll pay any amount to keep living. And your country?
UN Rep: We'll participate in the anticipated construction of Units 08 and up. There still is the problem of not having a pilot yet.
Gendo: That is not a problem. A pilot will be found. Now that the Angels have returned we have no choice but to defeat them.
UN Rep: Absolutely. We don't want a repeat of the Second Impact.
Switch to NERV. Juri is there with Misato, and they are observing while others are readying a transport helicopter. NERV workers are placing what looks to be a mobile power plug for an Eva into a transportation crate, and other workers are preparing to fasten the crate to the helicopter.
Worker one: Make certain the connections are secure!
Worker two: Moving mobile power supply into position now!
Juri to Misato: We're taking a mobile plug to Unit 02?
Misato to Juri: Just in case we need it. I don't anticipate it being necessary, but orders are orders.
Juri nods absently, writing something down on her clipboard. Then she repeats Misato's words to herself.
Juri (quietly): Being necessary...
We are now seeing the past again, the three pilots and Ruka in the Ohtori fencing gym. Asuka and Miki are watching as Ruka and Juri duel.
Miki to Asuka: They're great!
Asuka to Miki: If you say so.
Miki to Asuka: You don't agree?
Asuka to Miki: I don't see what all the fuss is about, honestly. No matter what Mikage-san and Akagi-san say, you don't need to be a duelist to pilot Eva. It's not necessary for us to do this.
Miki to Asuka: Then why do I see you practicing here after hours?
Asuka fumes, she didn't realize anyone else had seen her do this. Then she's perfectly proper again.
Asuka to Miki: Simple. If I am required to do this, I won't settle for being second best.
The duel ends, Ruka scoring a winning hit on Juri.
Ruka to Juri: You've gotten better. Soon I won't be able to keep up with you.
Juri smiles. It is the first genuine smile we've seen her make.
Juri to Ruka: Thank you, sempai.
Asuka to Ruka: What about me?
Ruka to Asuka: You've still got a very long way to go, Asuka.
Asuka looks ready to fume.
Ruka to Asuka: But you've improved several times over since we began. Soon you might be keeping up with Juri.
Asuka looks much happier. Juri glances over at Asuka.
Ruka to pilots: We're finished today.
The pilots leave. Ruka goes over to a duffel bag, pulls out a towel, and wipes off his face. He coughs, as he is doing this, and when he pulls the towel away, there are little bloodstains upon it. He doesn't seem surprised they are there. In fact, he smiles somewhat sadly at it.
We now see Miki, Juri, and Asuka having dinner together. They are wearing "normal" clothes.
Asuka: Two months and still we haven't actually done anything with an Evangelion.
Juri to Asuka: Are you getting impatient?
Asuka to Juri: Of course I'm getting impatient. If I wanted to learn to fence I could have stayed in Germany.
Miki to Juri: She's only saying that because she hasn't beaten you yet. If she had, all we'd hear about is how she was born to be a duelist.
Asuka looks at Miki in disbelief.
Asuka to Miki: Why...why...why you! You're dead, Kaoru-kun!
Asuka gets up and chases after Miki. Miki, having fun with it, begins circling the table. Juri, watching them, smiles as they circle around her and the table. For a brief second, they are standing in the exact image of the photo she keeps of them in her home. We hear a click, and then see Ruka walking in after taking a photograph of them. The flash makes Miki and Asuka stop.
Ruka: My, aren't we hyperactive today? Didn't I work you hard enough, Asuka?
Asuka to Ruka: You shouldn't be taking pictures of us without our permission.
Ruka to Asuka: Oh, but I wanted something to remember you by when my time here is done. I think that moment captured you perfectly, Asuka.
Asuka looks indignant.
Miki to Ruka: Are you leaving us soon?
Ruka to Miki: I don't know about that, but I heard that they are ready to begin testing the prototype. Which means I might not be seeing you as much.
Ohtori fencing gym. Asuka is alone, practicing moves and steps just like Miki said she was. As she finishes and leaves, we see Juri step into view. She has been watching Asuka just as Miki said he had. She smiles softly as she goes out the other direction.
Switch to NERV: Ritsuko is doing synch tests. Mikage is observing. Currently, since they only have the prototype, only pilot can be in the Entry Plug at a time. We are seeing Juri on the monitor. Ritsuko watches the synch-graph for a moment, then calls Mikage over.
Ritsuko to Mikage: See for yourself.
Mikage looks at the synch-graph, then to Juri's monitor.
Ritsuko to Mikage: This is Miki's synch rating. This Asuka's rating. This is Juri's.
Mikage nods after a while.
Mikage to Ritsuko: Is it always like this?
Ritsuko to Mikage: Without exception.
Mikage to Ritsuko: I see...and she surpasses the other two in every other category.
Mikage to Juri (monitor): Arisugawa-san?
Juri (monitor) to Mikage: Yes?
Mikage to Juri (monitor): Do you sense anything? Anything out of the ordinary?
In the Entry Plug, Juri seems completely at peace.
Juri to Mikage (off): No.
Back to Mikage and Ritsuko.
Mikage to Ritsuko: Let me know if this continues.
Mikage walks off.
Back to present day. Shinji and Utena are in their Plug Suits, coming out of the Entry plugs. Their tests are over. They are walking on the ramps leading away from the Evangelions.
NERV Tech 1 (off): Synchronization test of Units 00 and 01 complete.
Utena to Shinji: Ikari-kun?
Shinji looks over to her.
Utena to Shinji: Do you know what Ayanami does here?
Shinji to Utena: No. I asked Ritsuko once, and she mentioned something about Ayanami assisting my father on a different project. But she wouldn't say anything more than that.
Utena and Shinji are now off the ramps and walking together.
Utena to Shinji: Did you ever ask your father?
NERV Tech 2 (off): Beginning cooling protocols for Evangelion.
Shinji chuckles and shakes his head.
Shinji to Utena: Ask my father? You're kidding, right? We're talking about a man who has surrendered all parental responsibility to Misato. I stopped making any effort to speak with him a while ago. Even if I did, he wouldn't speak with me about it.
Utena to Shinji: I'm sorry.
Shinji shrugs. He honestly doesn't look bothered.
Shinji to Utena: It bothered me for a long time, but I think I'm moving past it.
Utena to Shinji: I remember Ayanami coming in here once a few days before I did. I guess I assumed she was one of the pilots.
Shinji to Utena: You haven't asked her?
Utena to Shinji: No, with the Angel attacking and all these tests I haven't even seen her in a while. I just remembered about it now.
Shinji to Utena: Say, on the same subject?
Shinji to Utena: You live with Arisugawa. Has she ever explained why she wears one of these-
Shinji holds up the hand with the Rose Signet.
Shinji to Utena: -but isn't one of the pilots?
Utena shakes her head.
Utena to Shinji: I hadn't even realized she wore one. I guess I never got a good look at her hands in the time I've spent with her.
Switch to Misato and Ritsuko having drinks in NERV's lounge.
Ritsuko to Misato: All set for the rendezvous tomorrow?
Misato nods, taking a drink.
Ritsuko to Misato: Which pilot are you taking with you?
Misato to Ritsuko: Shinji. I'd like to spend more time getting to know Utena, but at this point, I'd rather her have some more training time. She needs it. Besides, Shinji deserves a little time off.
Ritsuko (playfully) to Misato: You could always invite her to live with you too.
Misato to Ritsuko: You might do the same, you know, Rit-chan. I bet Tenjou would give you better conversation than your cat. Besides, I've already had her moved once. I'm not going to force her to relocate again unless she can't get along with Juri, and they seem to be doing alright so far.
Ritsuko looks at her drink for a moment.
Ritsuko to Misato: Mi-chan, are you taking Juri with you tomorrow?
Misato to Ritsuko: I had planned on it. You seem to disapprove.
Ritsuko to Misato: You do remember what happened right before Asuka went to Germany, don't you?
Back to the past. Juri is undergoing another synch test, Ritsuko is observing. Ritsuko pulls out her phone and makes a call.
Mikage (off): Mikage.
Ritsuko: Same results.
Mikage: (off) Understood.
Ritsuko closes her phone. We see the monitor before the scene switches. "Synchronization Test Subject: Arisugawa, J." The meter is stuck firmly at 0%.
Switch to Ohtori fencing gym again. Miki and Asuka are there talking quietly.
Miki to Asuka: Can you believe it?
Asuka to Miki: I know, first Tsuchiya-sensei dies, and now this. But, I always knew I would win in the end.
Miki to Asuka: That's not fair, Asuka-san! You haven't done anything.
Switch to a scene of Juri and Mikage. All we see are their silhouettes, we identify them by their hair, which is colored normally. Juri is wearing her fencing gear, and is slumped in a chair. Mikage is standing over her. They do not move throughout the scene. The view slowly pans backward the whole time, starting on Juri until we end with both of them in the picture.
Mikage to Juri: Essentially, there's nothing that can be done about it.
Juri to Mikage: I...I don't understand. That's the only reason?
Mikage to Juri: I know it must seem insignificant to you.
Juri to Mikage: I don't know if that's the word I would use...
Mikage to Juri: Arisugawa-san, you're practically perfect. In every other way you exceed the others. But if Eva won't synch with you, then you obviously cannot be her pilot.
Juri to Mikage: Can't I have a second chance? I've devoted so much time to this...
Mikage to Juri: I honestly don't see what good that would do. The Magi have run endless theories on this, and they all come to one conclusion. The Evas will only synch with those born after the Second Impact. And you were born-
Juri to Mikage: One day before the Second Impact...but it's just one day. How can one day be so important? It's not even a full day, not even twenty-four hours.
Mikage to Juri: It apparently means everything to Eva. Honestly, taking into account what happened to the older test subjects, like Ikari Yui, I'd say you're very lucky to have even come out of the Entry Plug in one piece.
Juri to Mikage: But, I don't understand. I was selected. You told me that I was one of the only ones that matched your requirements. Didn't you know about this already?
Mikage to Juri: I won't lie to you and say we didn't suspect this would happen. That Eva will not synch, not even to a negligible degree, with you proves that suspicion correct.
Juri to Mikage: It's only one day...not even a full day...
Mikage to Juri: Which is all that matters. To be blunt, Arisugawa-san, it would take a miracle for Eva to synch with you.
Juri to Mikage: Is that it, then? Am I now useless to you?
Mikage to Juri: Not necessarily. You know what it is we're doing here. I doubt you could simply walk away from it, forget what's happening, and resume a normal life. Tsuchiya's unfortunate death leaves an opening for a trainer, and you've not only been through the pilot training but you are also a master duelist.
Scene changes. Juri is walking into the Ohtori fencing gym where Asuka and Miki are waiting. Asuka, for whatever reason, can't resist saying something snide to cement this little victory over Juri. As she moves into a dueling pose, she smirks.
Asuka to Juri: Don't worry, Juri-san. You can always hope for a miracle.
Juri looks at Asuka blankly, hurt beyond description that Asuka would use Juri's own words to wound her like that.
Juri (off): You'd best hope for a miracle then, Asuka-san.
Mikage (off): To be blunt, Arisugawa-san, it would take a miracle for Eva to synch with you.
Juri's expression steels, and she suddenly looks at Asuka with the same hard look we've seen her give others. She moves into position to duel Asuka. They duel, and it's not even close. Juri decimates Asuka in seconds, far quicker than the last time Asuka challenged her. Asuka's epee goes flying into the corner of the room and Juri holds her own epee at Asuka's throat for a moment, staring her down. Then she walks off without actually touching Asuka with the tip of the epee.
Juri (leaving): There are no such things as miracles.
Miki watches Juri go, and looks at Asuka. Asuka goes and picks up her epee.
Asuka to Miki: What a sore loser.
Miki to Asuka: You haven't beaten her.
Asuka to Miki: Not with this (holding the epee), no. But she can win a thousand silly duels against me and it won't change the fact that I'm going to pilot Eva and she's not.
Miki to Asuka: That's cold, Asuka-san. She's your friend. She would have never done anything like that to you.
Miki leaves. As soon as Miki leaves, Asuka's expression changes from haughty to sad. She looks at the epee, then back to the door.
Back to present day. Misato is driving Shinji and Utena home. It's now night.
Misato: It was shortly after that that Asuka went to Germany, and I returned here and took Juri under my wing. So much talent being wasted as a mere trainer, since at the time, Miki was the only pilot in Japan and he'd already gone through anything Juri could have taught him. All she could do was improve his dueling skills, and she felt so unnecessary to everything that I couldn't let her languish like that.
Utena to Misato: That's such a sad story. Did they ever make up?
Misato shakes her head.
Misato to Utena: I don't think so. I think they saw each other a few more times before she left, but Miki told me it was only as teacher and student. Juri has never forgotten and Asuka has never apologized.
Shinji to Misato: Miki never mentioned any of this.
Misato to Shinji: I don't think he wanted anyone to think of Juri as a failure. Miki and Juri remained close after that. You probably shouldn't let on that you know either.
Shinji: So that's why she's so sensitive about anything dealing with piloting Eva.
Misato: Yes. It seemed to lessen as time passed, but with the Angels actually here now, I think she feels even more useless than ever. You two are living out the dream she was promised and denied.
Scene switch: Utena being dropped off, Misato's car driving off. Utena walks into the building. We see the door to Juri and Utena's apartment opening from the inside, and then Utena walks in. There is very dim lighting. Utena looks in to see Juri has fallen asleep without making it to her bed. She's asleep at her desk, arms crossed and head upon them. Her locket is open, on the floor. Utena quietly walks over and picks it up. Before placing it next to Juri's hand, she glances at the picture inside. Utena looks a little surprised, then sad as she looks at the sleeping Juri.
Focus on the locket in her hand. The picture inside is of course, Asuka.