Mr. Tines: The butterfly emerges from the chrysalis.
midoriyoh: This episode was an impressive journey. (Continued in additional comments below)
Additional Commentary
midoriyoh: The first scene sets the stage by presenting the idea of Instrumentality - humans cannot be satisfied, because our happiness depends on being wanted and needed by others, which is never secure, because we are independent of each other. That's why we need to lose our individual existences and become a unity, so that the insecurity that comes with being separate beings may disappear.
We then take a closer look at the precise way Shinji seeks happiness, and from this angle we reach the topic of running away - we find out that it's something that Shinji refuses to do because it makes others hate him, which is what he fears the most. This is analyzed deeper in Scene 03 - this desperate fear of being hated by others stems from his lack of self-acceptance. This is why Shinji seeks others' approval so hard - since he has none to give himself, he can only get self-worth by having it given to him by others. This is the natural outcome of a self-hating personality. The most effective way to make others praise him is by piloting the Eva, and that's why he ties his whole identity to this. Seeing others praise and accept him soothes the self-hate and is the thing that makes him most happy. But this happiness is very fleeting and uncertain - hence, anxiety. This is the conclusion that we reach in the beginning of Scene 05. We have descended to the source of his troubles - now is the time to resolve them and for Shinji to create a new self-image.
Shinji wants a more permanent source of worth, and Yui tells him openly - "Only you can find your own worth". This makes Shinji wonder about who he is, and he reaches the realization that the way he is seen by others, accepted or not, is something separate from his own self. It's only a representation in another person's mind - something independent from him, and not accessible to him. It's foolish to base your self-worth on it. Shinji's actual self is not accessible to others either, only to himself, and for this reason it's foolish to "outsource" the job of making himself understood and accepted to others. Shinji accepts that he is the only person that can truly give Shinji worth, but a new problem appears - he is a very imperfect person, so why should he value himself and be good to himself? The answer is that reality of himself at the moment isn't permanent - it's very malleable, because world itself changes, but more importantly because he has free will, which allows him to shape reality and change it, both inside and outside himself. None of his imperfections are inherent parts of his self - they are merely facts about him at the moment that can change, and he has the power to change them. "So, take care of yourself".
One more topic is touched at the end of Scene 07 - while Shinji's free will allows him to define reality, there is a reciprocal relationship - he needs things independent from himself to define him and shape him by being different from him. To put this in other words, the existence of other people allows one to exist more fully than if one were alone. Scene 09 has some more talk about the malleability of reality, and to double down on the theme adds that the perception of this reality is itself malleable. Our understanding of the world is imperfect and shaped by various influences, which makes basing your self-worth on what others think of you even more foolish - in truth, you aren't even basing it on what others think, you are basing it on what you think others think! As irrelevant as it would be if others hated Shinji, that's not even true - it's just Shinji's imperfect perception of the world.
At the end of this all, Rei adds one more motivation by reminding Shinji that his lack of self-acceptance is harmful not just to himself, but to other people. The last scene consists of Shinji accepting his independent existence and thus rejecting the whole premise that Instrumentality was based on, at which point the stage around him collapses and congratulations follow.
