Notice all the time given to Misato in the OP. Her face and figure are so expressive, anguished yet beautiful.
Previous posts in the series:
The Beginning and Ending of Evangelion
Beware of spoilers…
Captain Misato Katsuragi is the individual in charge of Shinji. She is the one who picks 
him up in the middle of an angel attack to bring him to NERV. It is her job to keep him functional enough to pilot an Eva.
Misato is a vivacious, sexually attractive woman of 29. She plays on this to catch his attention even before she meets him. Shinji is a hormone-addled boy of 14, just entering the most heated phase of adolescence. The photo she sends him just screams of sexual tease. A teacher who was caught sending such a photo to a student would be summarily fired. A commanding officer sending such a photo to an enlisted boy would be disciplined and likely discharged.
But this is anime so we get to enjoy it risk free.
Misato picks up Shinji just in time.
Shinji’s first experience with EVA combat is traumatic. He is tossed into an EVA without a single minute of training. He is almost destoyed by the enemy “angel” when suddenly the mecha develops a life of its own and starts shredding and eating the enemy. The stress is so great he forgets the moments when the EVA took over in berserk mode.
While he is recovering from the emotional scars Misato discovers he’s going to be living alone. For Shinji who has a lifetime of living alone, it might have been the correct decision.
Misato would not understand this. In her mind, no adolescent boy would want to live alone. Of course, he’d be happier with a roomie. Doubly happy if that roomie were easy on the eyes. “Socials”, as I’ve come to call them, don’t have the foggiest clue about the needs of an introvert and seeing another person’s depression freaks them out.
Misato doesn’t realize she needs to be a substitute parent nor have a clue about how a boy feels about his mother-figure’s sexuality. He eventually learns to tolerate it.
She is his legal guardian yet flaunts her sexuality. Manipulation of this boy ought to be child’s play, she’s thinking to herself.
Shinji isn’t an ordinary boy. He doesn’t respond the way she expects. When Toji Suzuhara and Kensuke Aida (friends that Shinji manages to make at school) meet her, their response is What a babe to be living with!
Shinji is incapable of this full-bodied lust. Actively desiring a woman and pursuing her – or even just having a decent fantasy about it – is so far beyond his ken that he can’t express it. It will stress him instead of giving pleasure.
You see, since he doesn’t like himself then he can’t imagine anyone else liking him. What do you do when faced with desire but expressing that desire can only bring ridicule and rejection? For one thing, you isolate yourself from it as much as you can. You distract yourself. You masturbate a whole lot and then (maybe) feel guilty over it. You shut down emotionally. (I understand this completely. That almost perfectly describes the entirety of my adolescence.)
So he moves in with her. At home, she is an undisciplined slob, the exact opposite of what she’s like in the command center. She wears tight-fitting tank tops, drinks enormous amounts of beer and has a pet penguin with its own refrigerator. The anime uses this setup to provide a lot of fan service. After excessive cheerfulness alternating with frustration at his lack of spunk, she ships him off the bath. “Bathing is the laundry of life.“
Well, maybe not. Meet Pen Pen.
There is symbolism in the jar of toothpicks. Shinji is still new to puberty.
Misato is not shy about fan service. Shinji is not shy about it either. He acts like he is more freaked out by Pen Pen than some of the angels he fights. He stands there full-frontal for almost 30 seconds and Misato smiles straight at him without batting an eyelash. The joke escalates when she picks up a concealing beer to show a strategically placed jar of toothpicks that keeps it PG-rated. Give him a couple years and he’ll need the full beer.
It is just a visual joke. Comic relief. But it might tell us something. Misato has been there, done that and got the t-shirt. Nothing new to see here. Suggesting he might cover-up was entirely for his sake.
Next, we see Shinji in the bath, completely calm. The embarrassment simply vanished. “I 
guess Misato is a good person.” This is telling us something and I’m not sure what.
He’s not fantasizing over being seen naked by a hot babe who didn’t seem to mind. Nor is he fretting about how Misato will hate him for this violation of social protocol. Both responses are realistic for a 14-year-old boy and the fretting would fit him perfectly. Instead, he says the tub just brings back bad memories and we see quick flashbacks of Gendo and Rei.
Gendo and Rei, both bad memories for Shinji.
OTOH, Misato is wondering if she’s being too “transparent” in her cheerful act. Is the facade really too facile?
Misato doesn’t know how to approach him. It is her job to keep his morale up and she really doesn’t have a clue. She has no other tools in her kit besides sexuality, exaggerated cheerfulness, and military discipline. It looks like he’ll be functional for an EVA again – but why doesn’t that make her happy?
Shinji finally gets a bit of training. He’s doing well, mainly because he is exactly following instructions, not because of any natural skillset.
Another EVA mission. Another fight. Shinji does exactly what he was trained to do – fire repeatedly at the center of mass to penetrate the enemy’s “AT” field. However, in the real world, this kicks up a huge cloud of dust that obscures the target. He doesn’t know how to respond and the EVA has its gun destroyed, is knocked onto its rear, armor penetrated by tentacles and thrown. It is an inevitable result of “virtual” training and a soldier who has no natural tactical skills.
Shinji’s world and welcome to it.
This time two of his classmates sneak out to watch it and are almost killed. Misato tells Shinji to let them into the plug with him. Dr. Ritsuko Akagi, one of the senior staff there tells her she has no authorization to allow civilians into a plug and Misato does it anyhow. Dr. Akagi only sees expendable civilians who ought not to be there. Misato sees classmates who Shinji will protect, regardless of the cost. It is a lesson she learned during the first angel attack. The protective instinct is very powerful in this one.
What she is ordering him to do, right now, is retreat. But all he hears are her earlier words, Don’t run away.
The Captain orders her soldier to retreat but it doesn’t get thru. Running thru his mind is the first order she ever gave him. Don’t run away. Not from yourself, not from your father, not from anything. Shinji himself becomes the berserker and with time and power running out, he launches a suicidal attack on the angel that destroys it just as his own power zeroes out.
Afterward she dresses down Shinji for violating her orders. It is an irony, as she herself violated Dr. Akagi’s order. Recovering from the stress, all Shinji can do is repeat “Sorry” and reiterate that a) he won and b) he doesn’t care if he dies. Misato misinterprets this to be an expression of bravado. He isn’t saying that he doesn’t fear death in the line of duty, he’s saying he doesn’t value his life.
Now she gets it…
Shinji stops going to school. Then goes missing entirely, leaving behind a note of
resignation. He rides the train, sleeps on benches and wanders thru the city, plugged into his music on permanent repeat. He is going thru a mental breakdown. He happens to find his classmate, Kensuke, playing soldier in a field. They talk.
And then NERV security catches up to him in that field to boot him out of town. If you don’t work here or have family who works here, you can’t stay in Tokyo 3. Gendo isn’t keeping a useless son around, he has to go.
His friends catch him at the train station. That is where all the people leaving town go and many have fled the fear and destruction. They say their goodbyes. Shinji makes a kind of final confession as he’s being dragged off.
But… it isn’t over yet. The security leaves after he’s on the platform. (I’m not sure why, after they forcibly dragged him there.) The train arrives and the door opens. Just then he remembers three kind words once Misato said to him and he just cannot get on the train to leave. His bond with Misato is too great.
Shinji has successfully learned to navigate other hedgehogs without too much mutual pain, even if it took destroying half the outer city to do it.
We all know that she ultimately offers her body to him many episodes down the line and he refuses. It was her ace in the hole. The question remains if Misato realizes she is a mother to him and not just another hedgehog.
Later posts:
Rei Ayanami is Broken. Shinji Wants to Fix Her
August 7, 2019 at 11:49
Wow! It was a stunningly well-written and well thought-out blog post! Thanks for sharing your work! 🙂
July 25, 2019 at 07:16
This was a really great post to read. The relationship between these two characters carries a lot of the episodes in Evangelion but doesn’t get nearly enough attention. Really enjoyed reading this.
July 25, 2019 at 20:37
There is so much to get into with Evangelion. I’ll probably talk about his school friends next. Then there’s Asuka and Rei, the other important people in his life. Later there is Kaowru and then back to Misato. His relationship with mother EVA. And the notorious ending.
He is building up a harem of sorts
The last screengrab almost tells the entire story right there. Misato is a terrible mother and were she to become a “good” mother, that would be the end of shaving Shinji into an EVA unit. She’d be a great lover, but that route is closed for now. It would overwhelm him and leave him emotionally swamped.
I think she’s walking a fine line between Hot Babe Who Cares and Captain Katsuragi. But just enough Mom – or maybe Big Sis – is creeping in to mess with her. I think she needed to add a lot more Mentor and Therapist into the mix but those are not in her repertoire.
July 25, 2019 at 20:50
I think everyone in Evangelion could have done with a local therapist but clearly dealing with peoples mental health issues was not high on their agenda.