It seems it was yesterday when I wrote an extended essay regarding the essential and critical relationship of Asuka and Shinji in Evangelion for the last time. However, seven years have passed. The last time I wrote it, I did so on Tumblr, so I have posted this on Tumblr too. You can go there if you find it more friendly to read it there. Besides, I wrote it on Reddit, albeit in two parts. You will find the links below:
Link to tumblr: https://petitfanboy.tumblr.com/post/662058193975951360/comprehensive-and-in-depth-analysis-of-asuka-and
Link to Reddit PART 1 (Introduction to Chapter 3): https://www.reddit.com/r/asushin/comments/pmdthq/comprehensive_and_indepth_analysis_of_asuka_and/
Link to Reddit PART 2 (Chapter 4 to the end): https://www.reddit.com/r/asushin/comments/pmdxcy/comprehensive_and_indepth_analysis_of_asuka_and/
My idea here is to write, in general lines, about the relationship of Asuka and Shinji in the last movie and the ending and its implications in a more detailed way. I will use different analyses I have read so far besides mine, and you will find the links to all of them in the text.
I have tried to maintain an analysis that follows the narrative plot and what I believe is closer to what the director wants to express. However, as Anno himself has said multiple times, his work may inspire different feelings in different people, so I understand where the differences might come from and, in no way, this is intended as a confrontation to other opinions and theories.
Please, let me start with an introduction.
Introduction
While a lot has changed for me in these years, my view of A/S relationship in the whole Eva universe, including their dynamics, meaning, and canonical aspects have not changed.
Long story short, A/S represent core aspects of the message Evangelion wants to transmit: The Hedgehog's dilemma, the fear of connecting and rejection while having a strong desire to be loved and understood, and finally, the pursuit of happiness. Asuka and Shinji are opposites on their outside and equals on their inside. A perfect match for exploring those issues.
RoE makes clear their similarities:
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Evangelion arrives at a fulfilling conclusion at the end, showing us how it is possible to overcome the abovementioned problems. To depict that, it always involves resolving the different issues Asuka and Shinji have between them, becoming closer, opening to one another and, probably and eventually, staying together.
Evangelion portrays that resolution using scenes showing the exact moment of the change in A/S dynamics, the moment when both pursued real connection starts. What happens after that change is unknown, but the intention is clear: once they begin to make an effort, they have the chance to be happy together.
Before the release of 3.0+1.0, different spoilers and youtube video titles ruined my life, as I suppose that happened to some of you. It had such a significant impact on me that it is hard to define with words. Not because I was an angry asushin fanboy as some might classify me, but because, had it been confirmed, it would have meant that the message that Evangelion has been constructing since its first airing was shattered to pieces. I could not accept it.
At that specific moment, the Eva Extra Ex manga came and saved me.
I cannot highlight enough how important this manga was and still, it is. For me, it represented a call from Anno himself, saying: Do not worry, Evangelion is going to keep being Evangelion. I still recall the endless discussions on the internet when 3.0 came out about the effect of the time-skip, in what lousy state the relationship between Shinji and Asuka was (or if it was even inexistent!) and how Evangelion was going to transmit another message in the end. For me, there were always precise moments in 3.0 that pointed against those conclusions. But with Eva Extra, everything changed. It tied aspects of 2.0 and 3.0 very nicely and allowed us to discover more regarding Asuka's feelings and motivations.
With the first interaction in the manga between Asuka and Mari, we see that Asuka still has (deep) feelings for Shinji. As the story progresses, we see how Asuka reacts to Mari's teasing and how unconvinced Mari is of all the bravado that she displays. A/S relationship, alongside their communication and hedgehog's dilemma related problems, still existed in the present timeline of the events of 3.0 and 3.0+1.0.
God's in his heaven all right with the world.

Chapter 1: The houses of healing
Instead of speaking of every Shinji/Asuka interaction scene, I will try to make this analysis lighter by talking about how it progresses across the film and focusing only on key scenes.
The film's first part explains how Shinji achieves healing after understanding how people around him are friendly, which is a big difference from EoE. In EoE, it was impossible. Shinji was left hurt and without any option to heal. He ultimately achieved healing through his experiences in instrumentality, leading to the ending and the hope/love message we all know in One More Final: I need you.
This process, this healing, happens in a precise location. That is the reason for the chapter's title. I took the liberty of naming this first chapter as the eighth chapter of Tolkien's book The Return of the King. But, what place is it?
Initially, Shinji is taken to Toji's house. While that place suits Rei, who will understand the basic meaning of life and being human, Shinji makes no progress there. Interestingly, Kensuke sees how Shinji is not making any progress and suggests he should go with him to his house. Why? It is driven by his new parental role, reminiscent of Kaji. He thinks why Shinji is in such a state and understand his needs at that moment. Besides, with or without knowing it, he reunites Shinji and Asuka under the same roof and the same parental figure.

I cannot say that he willingly wanted to reunite Shinji with Asuka, although I am sure he thought it was a direct consequence of carrying Shinji with him, so he was happy with that idea. As we know from 2.0 and the original series, their friends are the ones who notice Asuka and Shinji bond, so it would not be strange that Kensuke wanted to reunite both of them.
With or without Kensuke's will, bringing Shinji to Kensuke's house mirrors Misato's apartment, but with a male figure as the leader (i.e. A Kaji instead of Misato). It is a comeback to better times. Kensuke takes the parental figure for both Shinji and Asuka, as Misato did when Asuka moved in 2.0 for both children. This time, Asuka is the one who is already living there (previously it was Shinji), and Shinji is the one who arrives later. In 3.0+1.0 Misato cannot fulfil her maternal role anymore, as explained later in the film (and redeemed at the end).
Let me linger on this parallel. In 2.0, when Asuka arrives at Misato's house and introduces Asuka to Shinji, we have the romantic comedy scene of the shower a few minutes later. The scene makes us understand that they feel some attraction to each other, albeit in a very early stage (and introduces PenPen to Asuka). Time forward, this first interaction is repeated in Kensuke's house. When Shinji arrives, he finds Asuka naked after having a shower. This time, no reaction is seen from either part explicitly. Neither Shinji nor Asuka blushed or overreacted, but Asuka clearly states her disappointment, which shows us her desire that Shinji reacted, that Shinji expressed attraction towards her. A significant line that adds up to all the previous evidence about Asuka's persistent feelings for Shinji. What about Shinji? There is a minor detail. When he sees Asuka naked, he stares at her with a glare that is just a mix of emotions. Although it is difficult to tell what he is thinking, Asuka is directly opposite him, and he can see both the DSS choker and her body. However, he only notices the choker when she wraps herself with a towel. Draw your conclusions.

It is after this shot that Shinji notices the DSS choker
From that point onwards, we get a few scenes representing the problem Asuka and Shinji have communicating and how alike they are. When Shinji throws up for the first time, Asuka explains to Kensuke why Shinji behaves like that and shuts himself off. However, she is doing the same, playing with her console. Asuka's video game is Shinji's SDAT. Asuka hates the behaviour of Shinji because she sees her flaws in him.
Despite all the façade, she tries to communicate and help Shinji repeatedly in the coming scenes, checking on him on several occasions. Whenever she does that, the movie clearly shows us that she has abandoned her Shinji-like behaviour, showing us the console turned off.
Asuka and her videogame
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— twitter-user (@username) date
The climax of their conflict is the force-feeding scene. But before analysing that scene, let me tell you a few more details.
I believe that the mirroring of Misato's apartment is portrayed through other details. For example, the name KenKen might have been chosen in honour of the missing companion from Misato's apartment: PenPen.
Furthermore, while some people might find odd the tendency of Asuka to be naked, this is driven by her disgust with her own body, which is shown in the Eva Extra manga. Finally, to enforce the idea that the relationship between Kensuke and Asuka is different from the one that she and Shinji have, it is essential to notice how Kensuke calls them. He calls them by their surnames, Shikiname and Ikari, placing distance between them.
Let's return to the force-feeding scene. In that scene, Asuka wants to help him, which is why she feeds him, and at the same time, she explains her frustration regarding the lack of reaction and understanding on his part. The conflict between them is portrayed similarly to the Eva 03 incident in 2.0
Visual comparison
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She is trying to understand him, and she tells him rather precisely why she thinks he is in such a state. She only wants him to reciprocate that understanding, and she wants him to think and explain why she punched him after seeing each other after 14 years. I must highlight the punch's importance. It summarises their communication problems, their conflict. Eva clarifies it in 3.0 using the same parallelisms as other communication problems, like Gendo and Shinji.
However, we know how she feels. The Eva extra manga gives us that insight. She has feelings for Shinji but hates his inaction due to his internal struggles. The hedgehog's spikes have been replaced by a punch. If they can talk about the punch, they will start communicating.
From an external view, Shinji reacts to being force-fed in a way that probably is not what Asuka wanted. Shinji leaves the house, followed secretly by Asuka, in another display of how Asuka feels internally. It is another parallelism with Misato's apartment, again with a reversal of roles between Shinji and Asuka.
Parallelism
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However, we will learn in future events that Shinji started to think about what Asuka told him at that moment, so he listened to her.
From this point onwards, Shinji will deal with his thoughts and come to an understanding with himself. It is not achieved alone, but with the help of Rei and, although not directly, Asuka. She is the one who directs Rei to the place where Shinji is and continues checking on him to see that everything is going fine. She is there.
Asuka cares
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— twitter-user (@username) date
When Shinji grows up and maturates, we have the first bidirectional communication attempt between Asuka and Shinji. While she asks Shinji if he feels better, he responds with only sounds. Yet, this is the first time they have tried to talk about their respective problems and emotions calmly. We will see this pattern repeat itself several times in the movie: Shinji grows a bit, and then Asuka opens herself another bit. It is very interesting to see Asuka's glare. Asuka is drawn with that glare whenever she is looking at Shinji in a positive/concerning him way. We will return to that later. Besides, she speaks to him without looking at her console.

First communication attempt - Question

First communication attempt - Answer
All this healing process ends in a sentence that is easily overlooked. The night Kensuke is discussing with Asuka the plans to return to the Wunder, Shinji comes home and says, "I am home". It is the reflection of Shinji's complete healing. Thanks to his growth, he has found a new place where he belongs once more. It let us understand why he will consider that this place is important for Asuka too. Both have suffered the same parental love deprivation, lacking a place where they truly belong. Finding a place that they can call home is part of their way to happiness and usually happens before both connect.

Tadaima
The film also let us see how Shinji heals, comparing it with the healing of one of the village's dogs
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— twitter-user (@username) date
Now, Shinji is ready to go with Asuka to the Wunder and start a transformative journey for himself and those around him. But first, let me post a few more details, some of which I had not noticed until doing some research on the internet:
1. Visual comparisons that highlight the similar role of Kensuke as Kaji (Parental role)
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2. Asuka's scarf to hide her DSS choker.
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3. The possible futon share between Asuka and Shinji, showing how she cares about him
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Chapter 2: A trip in the Wunder
The most relevant scene for their relationship in the Wunder is Asuka's confession. However, there are a couple of interesting interactions before that. The first one is the display of Asuka's jealousy of Sakura when she sees her interaction with Shinji, saying, "Are you his wife?"
The second one happens when Asuka meets Mari. While loaded with fanservice, this interaction is not trivial. Mari's teasing is an essential element in the Rebuild series, even more knowing how important the character of Mari will become at the end. She seems to be aware of Asuka's real feelings, and we know from the Eva extra manga that she tries to push Shinji and Asuka together, which I will come back to later. Asuka replies to Mari's teasing that Shinji "does not need a lover, he needs a mother". This sentence is a double edge sword. First, it shows Asuka's interest in Shinji as a romantic partner, given her deception, and actually, Asuka is saying this sentence while she is playing the videogame, so probably she is hiding her feelings, shutting herself oof the world as Shinji used to do. Second, it shows the problems they face: Communication and maturity. Maturity, because Asuka feels that Shinji has not changed as she has had, and communication, because as we will soon know, Asuka also wants that figure in her life. However, it is not true that Shinji has not grown up. It is just that they have not tried to communicate again, and thus, she does not know about Shinji's recent developments


Asuka does not stop playing in all the scene
Everything will change when Asuka faces the reality of possible death. Before the "final battle", she decides to reach out for Shinji. After Mari introduces herself to Shinji in an awkward way that will be important in the ending, Asuka repeats her question. In reality, she asks if he has thought about her, how she feels and everything she has gone through. To Asuka's surprise, Shinji answers the question, blaming his inaction. Taking this as a partial sign of maturity and growth, Asuka starts opening herself, although not wholly, a sign that Shinji's answer might not have been entirely correct. Besides, her body language is similar to the previous lift scenes in Evangelion, where we know she hid her real emotions.
She will equal what to tell Shinji to Shinji's growth. Therefore, she explains to him how she liked him 14 years ago, but not how she feels now. Furthermore, she leaves before Shinji can reply to her statement, leaving Shinji staring at the floor thinking about her words. So, it is Mari again who makes us understand that this has been a sign of communication that goes in the right direction. She congratulates Shinji and stimulates him to continue like this. Again, Mari is trying to solve Asuka and Shinji's problems. Mari says goodbye in Chinese to Shinji (perhaps, a way to tell us that the spell of goodbye works, as they meet again later) and goes to do the same with Asuka, asking her if she feels better. Mari is trying to make Asuka see that opening herself to Shinji will bring happiness to her too.
Nevertheless, we must not forget that the short confession happened because Asuka thought this might have been the end. In a sense, it almost was.
Chapter 3: I need you
This chapter starts after Shinji and Gendo have resolved their issues. As I explained before, the need of resolving their parental matters will be critical to both Shinji and Asuka. The same happened in EoE. Asuka gets to know her mother in her battle against the mass-produced Eva, and Shinji learns about his father's plans and mother during instrumentality. After those experiences and their other interactions through instrumentality, they arrive at the I need you scene where they open to each other.
Gendo gets off the train, and the control of instrumentality is handed over to Kaworu. While Gendo was willing to sacrifice everything for his sake, the growth of Shinji reaches its maximum at this point. Shinji decides to take the reversal role of his father. Even if he is heartbroken or it is a hard and not a pleasant experience, he wants to help Asuka and those who were nice to him. This is the transformative journey that Shinji accomplishes in RoE that marks a completely different path from NGE+EoE.
I worded the sentence highlighting Asuka because those are the literal words of Shinji, naming Asuka as an individual and using the Japanese word "minna" for the rest, which could be the rest of his friends or even the rest of humanity. Shinji has learnt that he must give without seeking anything in return. He must stop thinking about himself only. He is going to help their friends without any positive repercussions on himself. As he later will explain, he plans to rewrite the world with the new spear given by Misato to get rid of the Evas and what they represent, stopping the cycle of suffering that comes with them, and let their friends live a happy life.
Symbolism of the spear
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Interestingly, he does not explain this to Asuka and only mentions it to Rei, with some hesitation, which is what prompts him to tell her that Mari would come for him eventually. That behaviour is because for getting rid of the Eva and rewriting the world, he needs to impale himself with the spear inside Eva 01. While we do not know for sure the effects on Shinji, the way it is portrayed resembles a willing sacrifice, a person opening himself to that terrible outcome for a better benefit for their friends. Besides, we must not forget that the sync rate of Shinji with his Eva was infinite at that time, so probably the expected outcome would be the death of the pilot and he knew about that.

The sacrifice
This situation is what gives us an essential context for understanding Shinji's actions. As Asuka earlier, he also thought that he might not return, there would be no tomorrow. But let’s see what happens with Asuka and Shinji.
The first to be saved is Asuka. As some sort of guardian for Asuka (and Shinji, and even Asuka/Shinji relationship), Mari reminds Shinji before he leaves her entry plug in the anti-universe that he has to find her. And he does.
There are many iconic and meaningful landscapes in Evangelion. Still, none of them has the symbolism, meaning, emotional associations and beauty as the beach where Shinji and Asuka laid at the EoE has. Although it is not the same beach and there are different details, the scene's meaning is clear. It was the scenario of One More Final: I need you. Thus, the location evokes that meaning, where Shinji and Asuka connected and expressed their emotions and feelings in EoE. To increase and highlight that intention, the first shot we have of the landscape is a full white moon, a remnant from the N3I. The moon has always been a poetic figure for love, and it brightens the sand creating the white beach. It is the perfect scenario to share an intimate moment.
Then, a saved, Eva curse-free Asuka awakes. The first sentence references the fact that the curse of Eva is lifted, and she can sleep. As some people detail, the plugsuit is a combination of different ones. This phenomenon will repeatedly happen in the anti-universe. Long story short, as I do not want to enter the terrain of the time loops and different universes, I believe that the idea behind that symbolism is that Evangelion is a multiverse. The anti-universe might somehow connect them, and we can see them. However, the characters remain the same from the universe where they come from. Only those annotated in the book of life remember those other universes or RoE time-loops (which seem to affect only the RoE universe and seem not to be confirmed in the other universes), and probably, as Shinji is in charge of the flow of events, the bleeding in his memories is what drives those changes.
The fact that Asuka wears a plugsuit that is a combination of previous ones, does not mean that she is Soryu or several Asukas at the same time. She is Shikinami, and it is the first time that she is on that beach. Her background and memories are from the RoE timeline, as she does not express, as Shinji will do later, any perception of that phenomenon. The same goes for their location. While they are on a similar beach, it is not the same where Soryu and Shinji found themselves in EoE. It is probably the bleeding of details between universes that wraps the metanarrative message that gives importance to the scenery (that beach is where they connected and accepted each other both in EoE and in this movie, and the place will always symbolise that)
Even those aware of other timelines (Kaworu and Shinji at that point) can only remember that they met before or have a déjà vu feeling. They do not have a complete insight into what happened. I think that this bleeding of details gives an important message: All the universes of Evangelion exist. Soryu and Shinji's story from NGE and EOE has happened, albeit in another universe, part of a larger multiverse. In a sense, it is saying that NGE+EoE is as canon as RoE, something essential to maintain coherency. The difference is that they happen in different physical planes of space and time.
Let's return to the fact that a grown Asuka is on the beach. The camera plays, repeating the same shots as in EoE, linking both scenes thematically again. Moreover, the visual links expands to other couples in Eva.
Visual comparison
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Here, Shinji sits next to Asuka, with his arms around his legs and a completely different gaze, making clear Shinji is happy to see her. The events follow this path:
1. Asuka sees Shinji next to her and calls him "Baka Shinji" in a not mean way. A way that shows us that despite calling him "Baka Shinji" time and time again, that did not mean that she truly hated him.
2. Shinji verbalises his happiness to see her again and says thanks to her for letting him know her feelings previously.
3. Shinji reciprocates the same feelings, using the past tense. Why? Well, at least this time is more straightforward than explaining why he choked her. Shinji has several reasons for this: First, it directly answers what Asuka told him earlier. And second, he wants to save and return her to the Eva free world, and thus, knowing that he might not return, hides his current feelings.
4. Asuka is surprised that her feelings are reciprocated. She blushes and turns to her left, hiding her real feelings at that moment to Shinji. In the next shot, we see a happy, blushed Asuka smiling.
The reaction of Asuka and all the previous evidence from the movie and the manga make it evident that she still has feelings for him. With his body language, Shinji is also transmitting to us that he is hiding his true feelings. Besides, a past tense confession for Shinji makes no sense at all. Shinji has been sleeping those 14 years. For him, those moments where "he liked" Asuka are only a few weeks or months ago from this moment on the beach. We will get the last evidence that Shinji still has feelings for Asuka, thanks to Kaworu. He, who is aware of all the timelines and universes, asks Shinji whether he will feel lonely letting Asuka go. Shinji, with the same body language and a sad face, says no. We must link Shinji's behaviour to the fact I explained earlier. Shinji wanted to sacrifice himself for the happiness of Asuka and everybody.


Note the similar body posture and an opposite face expression to that on the beach
This links with another idea. The scene is fast-paced. Once Shinji confesses his feelings, he says goodbye to Asuka and the Kensuke sentence. While this might be a reminiscence of Asuka's behaviour in the Wunder, allowing him to avoid any reply that would have made things more difficult. However, his words are carefully chosen. We know from Rei's experiences in the village that "goodbye, is a spell of magic to see each other again. Despite his plans, Shinji's wish is to see her again
The meaning of goodbye: https://www.reddit.com/r/asushin/comments/p73bj5/the_meaning_of_goodbye/
Then we have the Kensuke sentence. I wanted to talk about this in a simple way. Asuka needed the same parental role as Shinji, and through her experiences in instrumentality, she finds that she has that part of herself fulfilled by Kensuke. However, things get complicated if we start to notice some details. The fact that Kensuke calls Asuka "Asuka" instead of Shikinami and that the doll with Kensuke inside of it appears in the Rei scene has raised concerns that the Kensuke who appears in Asuka's instrumentality scenes is in fact Shinji, helping Asuka to find her place in a future world without him and comforting her. In more detail:
1. All Asuka's scenes in instrumentality revolve around Shinji , nothing from Kensuke. It seems that Shinji wants to revert that and makes her conscious that she can find a place to belong and the parental role she needs, especially taking into consideration that he thought he was going to die
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2. She verbalises that she has no place to belong yet (despite living with Kensuke for some time), so Shinji wants to clarify that point for her.
3. It answers why Kensuke calls her Asuka and not Shikinami and why the doll appears again in Rei's scenes on the stage. Furthermore, it connects Asuka's memories with the beach scene, as it is after Kensuke says, "Asuka is Asuka" that she wakes up next to Shinji.
The original source of the theory for me was this video: https://www.youtube.com/watch?v=ZyATqdlnzZg&feature=youtu.be
In the end, from Asuka's instrumentality to the end of the beach scene, Shinji wants her to understand that she has a place to belong alongside the parental figure that she needs and that she is also loved by him, although he is going to let her go for her benefit. A true act of selflessness given his feelings for her. That is heart-warming and an actual act of love on his part.
Then, something happens amid the fast-paced scenes. The camera shows Asuka with an open mouth, sleeping(?) and Mari next to her. Wait. When did Mari come in? Why? I am not sure of the answers to these questions. It shows that Mari is more than we thought and has more knowledge about the anti-universe and what is happening. We do not know if this scene happens just after Shinji’s words or something has happened in the middle, as Asuka's expression seems not to match the last we see from her. Is there a deleted scene in the middle?
Mari says her goodbye to Asuka. Mari has been a bridge between Shinji and Asuka and a close friend to her. In some sense, and continuing the parallelisms between Shinji and Asuka, she has been her Kaworu

This shot is exactly the same as the one in 3.0 involving Shinji and Kaworu
Interestingly, Mari only appears to say bye to Asuka and not Rei or Kaworu. At the same time, Shinji only says sayonara to Asuka, the only character that does not have a handshake and a shutter closed. While there is no definitive answer to this fact, I believe it is crucial regarding the ending, as it will establish a continuity between the goodbyes and future gatherings, all directed by Mari, and that is why she appears probably (and she might be the one ejecting Asuka's entry plug).
After Mari's take care, Asuka wakes up in the entry plug and is ejected by Unit 13. It is important to note that Asuka leaves without any kind of voluntary movement. She awakes in different locations and is the Eva 13 who ejects her. We do not know Asuka’s opinion about this at any time, or how she feels about being saved leaving Shinji behind.
Chapter 4: The sacrifice is stopped
After Kaworu and Rei's scenes, which I am not going to talk about, Shinji decides to carry out the Neon Genesis. We get to the moment where he is ready to sacrifice himself, in some sort of redemption of humanity's sins for creating the Evas and all the suffering that accompanied them. But then, Yui appears.

Yui protects Shinji and takes his place
She stops the spear, protecting Shinji, and takes him out of the Eva 01. Yui’s wish is that he can live in that Neon Genesis world where the Evangelions do not exist, where people, and Shinji, can be happy. This moment changes everything. The plot twist will allow Shinji and Evangelion to have a happy and hopeful ending, thanks to Yui's (+/- Mari) plan.
The sacrifice of Shinji's parents for the sake of their child redeems them from the emotional deprivation Shinji has endured all his life. Shinji, mimicking the last instrumentality scene in EoE, returns to the anti-universe, now alone.
Chapter 5: Mari to the rescue
Shinji waits patiently on a blue water beach. Slowly, he starts to fade away in the anti-universe, as there are no others to relate with. This concept was explored both in EoE and at the end of the TV series. Then, Mari comes with her Evangelion to rescue him and take him back to the real world, now the Eva-free world, as promised to Misato. This is very important, as it highlights that Shinji is not going to a parallel universe. He is returning to the same world where his friends are (Asuka for sure, Kaworu will meet him again too, and Rei, honestly, it is not so obvious where she decides to go in her scenes, but probably too)

Mari's promise. It might signal the replacement of Misato's role by Mari
Mari's last Evangelion is important too. Contrary to Kaworu and Rei, I believe it is how Mari and Shinji returned to the ordinary world (probably with its entry plug, like Asuka). We might never know that. Then, the next scene is the opposite scene from Asuka in the entry plug, but with Shinji. Now we see an adult Shinji in a train station.
There are different questions to answer to understand what is happening in the ending. However, I think that the film's conclusion is the same regardless of the answer to those questions.
The questions are:
1. Is the train scene set in the AU or in the real world?
2. Are Mari and Shinji the people we see coming out from the station?
3. Did Asuka arrive at Kensuke’s house?
I tried to sum up the different theories in simple pictures.
Scenario 1

Scenario 2

Scenario 3

Scenario 4

My personal opinion just after watching the movie was that the first scenario was the most likely. However, after seeing different analyses, I am not 100% convinced, but still I cannot give my support to other theories though.
The sources for the other theories are here
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And the fact that the pilots might be illusions come from this source: https://www.reddit.com/r/asushin/comments/pclvmi/if_the_ending_is_offensive_and_hard_to_understand/
As you can see, regardless of the answer to the questions from above, they always end up meeting again. While this is not explicitly shown in the movie, I strongly believe is the reason why Mari appears at the end scene. Mari is the beacon light that will guide him in this new world, and there is a lot of visual comparisons that prove this fact, comparing Mari to Misato, and knowing the role of Mari in Gendo and Yui’s life. Furthermore, a lot of people consider that the fact that Asuka is alone in the platform is a sign that she is there to be reunited with Shinji, as she has no partner and seems to be playing with something like her old videogame. All of this is enough evidence to stop thinking about this ending as “Shinji choosing Mari to live a happier life” or “to let go the past”.
Misato is replaced by Mari
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The role of Mari in Yui/Gendo life.
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A hint in her possible role with Asuka/Shinji
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I am sure that Mari will reunite Asuka and Shinji. She has been a bridge between them since 3.0, and the Eva Extra manga gives more insight into that respect. Besides, she did the same with Yui and Gendo, and there are a lot of comparisons between Yui/Gendo and Asuka/Shinji in a visual way throughout the series, mainly with her eyes. You will find Asuka glancing at Shinji with the same face and eyes expression as Yui did.
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While it would be interesting to know exactly how Shinji arrives there, the narrative conclusion that they will meet again, independently of what has happened to the world, will not change. This resonates with the title of the movie "thrice upon a time",as evidenced here:
https://www.reddit.com/r/asushin/comments/p5goe8/thrice_upon_a_time_hm/
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There have been multiple Evangelion universes, both with and without Evas (EoE ends with a world without Evas, as the manga does) and in all of them, all of them, Asuka and Shinji meet again. And this is really important, as now they can communicate and have the chance of growing together and be happy.
Conclusion
Asuka and Shinji are two sides of the same coin, with different defence strategies in the context of the hedgehog's dilemma. Despite their mutual attraction, they are incapable of communicating and reaching each other. In EoE, it took almost the end of the world and humanity to understand that it is thanks to not living with the fear of pain and rejection that we can understand and accept others, ultimately overcoming the hedgehog's dilemma. This is expressed by the caress of Asuka to Shinji in EoE. This loving gesture shows us that the characters start understanding each other and have the chance to be happy together. EoE ending is a message of love and hope.
A/S relationship will represent this conflict wherever they are portrayed, in a cycle of desire/attraction, which leads to conflict and a resolution with understanding and love once they learn to accept each other and start communicating. In EoE is quite visual and displays both of them together at the very end. The manga is less explicit and more hinted at, but the scene at the train depicts how they connect in that new world where they will understand each other.
Thrice upon a time is not an exception to this rule. The last scene of EoE and the manga that involves Asuka and Shinji is the moment they connect, communicate, and change the way they treat each other. In 3.0+1.0 their final scene together is the beach scene, where they confess their mutual feelings in what is a never seen before sincerity and openness between them. Then, a world without Eva is created (in EoE this is exemplified by the crucified Eva and in the manga is more similar to the movie) and we know that Mari will guide Shinji to a safe return to that Eva free world and a gathering with Asuka and his friends. Despite not appearing on screen, all the narrative of the movie, and the whole of Evangelion, makes us understand that they will understand each other more and more and will be more honest towards their feelings, giving them the chance of being happy. As a consequence of that, the leitmotif of Evangelion is repeated once more.
The message of 3.0+1.0 is not about letting go of the past because you have grown up or let it go to move forward. The message is that it is thanks to going through those good and bad experiences that life gifts us, accepting the chance of suffering pain, that we can mature and learn. This learning will make us understand ourselves and those who surround us more, making us love ourselves and others, having, ultimately, the chance of being happy, loved and finding a place to belong to.
And it is in the middle of this struggle, that the love story of Asuka and Shinji shines, reminding us that humans can connect and be happy. If they can overcome their problems, so will us.
Everybody finds love in the end.
One More Conclusion: Where is Anno's wife?
What a ride! I think I have written about almost all of Shinji and Asuka's interactions, perhaps leaving just a few ones at the beginning of the movie, and without the mention of Anno as Shinji or his wife as Mari in all the essay! While extremely popular, the theory that Mari represents his wife has many flaws and I still do not understand where it is based. From the character being designed without the supervision of Hideaki Anno to the direct denial from his wife, including that the theory does not match the narrative plot. While self-insertions and story developments related to personal experiences are not rare in storytelling, we cannot explain everything in Evangelion by metanalysis. While Anno's struggles with depression have shaped NGE+EoE, the development and growth of the characters in their own arcs are what matter when analysing them. Shinji might be inspired by his awful experience at that time, but as we said earlier, Asuka is shaped like Shinji, albeit with different behaviour. Therefore, we should accept that both of them are depictions of Anno and not only the masculine figure.
In the end, it is Shinji who rejects instrumentality, returns to the real world and is caressed by Asuka in EoE. The characters do that, not Anno. The same happens in this last scene. While the location of the train station and city is totally related to the director, what is going to happen to the characters in the context of the plot is the important thing to consider when analysing them.
From NGE+EoE to this last movie Shinji always grows and understands the path to be happy. This is not exclusive of the RoE saga because Anno has overcome his problems. Therefore, conclusions such as "now Anno is happier, so he wants Shinji to be happy" are not supported. What changed in RoE is that the growth of Shinji happens prior to the last impact and instrumentality, instead of growing after those experiences. This allows the portrayal of a lighter version of Shinji in those dramatic moments, resembling more a traditional hero who saves his friends, instead of letting them down and then coming to an understanding all together (because everyone shares a slice of the guilt cake) in instrumentality.
I believe that it would be more fruitful if we took into consideration his wife's work in the way that this tweet states , rather than engage ourselves in discussions about meta self-insertions.
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I hope my words have helped those who felt like me after the release of the movie.
Thank you very much for the time you took to read this.