In Neon Genesis Evangelion, the control centre really matters. I mainly mean to say that it has thematic significance, but I guess I’ll trot through its obvious functions in the drama first. It’s the location from which we see the reactions to the action. That means that it sets the parameters for the show during those monster battle segments, tells the audience stuff - “It’s a Sinker!” and so forth. The base is where we go to analyse stuff and raise our eyebrows (from behind the geeky spectacles of science) at the staggering power levels.
This high-tech setting lends a tone of shiny shiny scientificness. It robots-up the not very robotic mecha action, makes it feels more like sci-fi and less like some random colourful giants having fights. At the same time as providing this sci-fi sheen it also humanises the action. Eva uses this trick several times when the action turns really nasty, with the reactions to the rampages and brain-rapes bringing home the brutality.
Anyway, the watchers aren’t just there for our convenience, they’re actors in the drama. And their role as the ones who watch the action involves some pretty serious power-plays. On the one had it raises the hero above the others by having him act while they just talk. On the other hand it creates an array of interpersonal relations based in surveillance, which contain our hero.
Our pal Shinji isn’t making many decisions. He’s a drone in a high tech hive. Sure, we, who see him up close, know that as a human being he’s a neurotic mess - far from a fighting machine. But after school he goes to the fleshbot, everyone sits and scans him, and he tries to perform anyway - his actions defined by others.
So many heroes seem to acquire power on account of protecting something, which is a neat way of making killing people into acceptable social action. Violence can thus be disconnected from personal morality. There’s a difference of agency between one who acts violently after consulting their inner beliefs, and one who acts by consulting others for the ideal position. In that standard where the hero gains strength from protecting comrades it matters that they watch - their presence is a source of power because it suggests that the inner certainties of the hero are in sync with their own social world.
In Eva being the one elected to smash stuff up isn’t so great. Sure Shinji is saving everybody - but he’s being coerced into it, living in an environment designed for an emotionless doll like Rei. Where positively designed heroes step up and take on the mantle of representative of the people Shinji lacks that sort of moral certainty, and has to be constantly kept on course by those who watch him - by whatever means necessary.

It’s always clear that Shinji is a pawn. He has power, but his morality is confused, and the seemingly protective goals he is guided towards by authority figures are merely part of a greater scheme. Eva gives us the hero as dupe, communications means surveilance, a trap run by Machiavellians.
Thing is, Eva is about the human singularity. Cut past the giant dancing robots, the conspiracies and the charming Biblical wallpapaer and that’s it. And in that place Shinji would be completely linked with everyone. It’s pure communication, displayed as sexual. It is, in fact, the ultimate contrast to the regimented watching array with which Shinji communicates with the military scientists.
In Kino’s journey a nation where all citizens (telepathically) communicate everything becomes a nightmare - everybody hides away from each other, afraid of personal truths. Eva offers something like that, except that our personalities merge too - eliminating the downside of communication. And that’s a heaven, an enlightened state, if an inhuman one.
In Eva being human means having personal issues. When it asks whether we’d be happier as thinking goo it’s setting up an opposition between a society of individuals communicating and a collection of minds in unity. Whilst individuality may be the explicit issue it has to be remembered that the way in which individual relationships function is affected by social structures. When one person is the actor and the other the watcher there’s all the ingredients for a dysfunctional dynamic.
The command centre in Eva represents the future society presented in Eva. Shinji is significantly defined by how he is being watched. The scientific approach, the militarism, the rigorous analysis. The fact that it’s Misato (and, in the shadows, his dad) who approach him via that apparatus. He looks to them for his certainties, and they monitor his pulse. It’s a kind of nightmare. Not so creepy as the singularity of course, because it’s a set of social restrictions that parallel reality.
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