“The System,” some kind of deeply hidden procedure or agency, makes a great antagonist. Tell you why in a sec.
You see “The System” in a lot of places. Off the top of my head I can think of Revolutionary Girl Utena, Puella Magi Madoka Magika, and Wonder Egg Priority, and if I’ve got three while I’m sitting here drinking sake, there have to be thirty more.
You know what’s a good example? Seele, from Neon Genesis Evangelion. Let’s take Seele as typical (it pretty much is) and have a look, okay? What do we see?
The System is faceless.
Right? All you see of Seele is the backs of their chairs. There could be any sort of entity sitting in them.
The System works through minions.
Right? First Kaji and then Kaworu, plus whatever’s going on with Akagi, and finally the JSSDF. Seele sends each of them out there to take on NERV.
The System’s powers are mysterious.
Right? Seele can penetrate NERV with ease, remove Furutsuke and Akagi as it pleases. It seems to have something to do with the Angels but no one can really tell. It has sufficient pull with the Japanese Self-Defense Forces to get them to attack NERV, but what the pull is no one knows. Doo doo doo doo. It’s like something from the Twilight Zone.
That combinations of things makes The System a very powerful narrative device as an antagonist. Because it is faceless, you can’t point at any given character and say, “That’s the bad guy. I know it!” There’s always a question about who the system controls. That creates tension, right?
Because it works through minions, there can be indirect conflict with the protagonist(s), BUT defeat of the minion is not final. The minion is a surrogate; defeat of the minion is not terminal to The System pulling its strings. The System can always toss another minion out there. Are they done yet? More tension.
Because it is mysterious, no one knows what its powerz are. Seriously, who knew Kaworu was another Angel, right? How did Seele get their hands on an actual Angel? Who knows?
Any time you think, “Who knows?” the storyteller in you should think, “conflict.” And conflict is a good good thing in storytelling.
And The System has one more narrative plus as an antagonist: Everyone’s been screwed by it at some point. Sometimes the specific arm of The System has a name: The Internal Revenue Service; The Department of Motor Vehicles. Ooh, ohh, here’s a good one: The CIA! In my racket (university professor) the Promotion, Tenure, and Retention committee is a source of existential terror. (And yes, I have been screwed by at least one of those. I fought The System, and The System won.)
So it operates at two levels, the level of story (because it creates conflict) and the level of audience engagement (because audience members relate to the problem). That’s not a bad deal.
And since I’m not the only one – by any stretch of the imagination – to have fought The System and had The System win, when the anime protagonist fights The System and wins, it is a triumph not only for the character, but for the audience as well. You’re supposed to identify with the protagonist, if they are well-constructed. When they win, you win. Yay!
When they beat The System, YOU beat The System! Who can’t go for that?
HOW you beat The System, well, that’s what the story is about, right? Have a good answer before you start writing. Here are a few:
Your protagonist can be stronger than The System, but that’s a narratively poor solution. It means the antagonist was weak.
Your protagonist can have mysterious powerz of their own. One of the beauties of End of Evangelion is watching Rey Ayanami reinvent the world based on her newly-discovered love for Shinji. It is powerful emotionally.
Question: Who is Rey Ayanami that she has god-like powerz? Answer: Um, yeah, I dunno. (Formally speaking, she’s the clone who learns to be human because of her love for Shinji, which is powerful but doesn’t explain how she can recreate the world given that she’s a clone of a human being.)
A better way is to have protagonist beat the system by refusing to play its game. That’s how Utena works, right? Even after she is terribly wounded – literally stabbed in the back – by Anthy, the ultimate product of The System, Utena says, “Nope.”
Better than that: Have the protagonist twist The System against itself. (It’s like judo, if you think about it.) But how about Madoka Kamane using her one wish on joining The System to blow up The System?
I think the only real flaw in The System as an antagonist is that there’s a limited number of systems. The government. The church. Big business. A sinister secret organization. What else you got?
And because of that, you have to be careful with it. I mean, seriously: How many sinister secret organizations are there out there? In anime world it’s somewhere around a zillion. When your antagonist is a cliché, you’re hosed.
So be careful out there, people.
I always look at comments and feedback, and I’m sure I’m not the first to see what I’ve seen, so have at it. Just keep it clean and keep it on target…no personal attacks, okay? Thanks.
Confessions of an Overage otaku 
A bunch of writing resources and my local writing group recommend Debora Chester’s Fantasy Fiction Formula book, which says you absolutely need to have a single mustache-twirling evil antagonist for a fantasy/SF book to be successful.
That just seems unrealistic and unsatisfying to me. And it doesn’t need to be a globe-spanning cabal, Just something with hidden levels that influence what your character sees. It could even be an organization with a positive goal, going about it in a terrible way, like Orbital Children.
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I think I’m with you on that one. Book or anime, The System is an over-arching existential threat that doesn’t go away.
Excellent point about Orbital Children. The System doesn’t have to be bad, just antagonistic to be an antagonist. A lot of systems are by design built with good intentions – like the DMV, whose job it is to keep people from getting killed – but end up opposing the desires of the protagonist, in the DMVs case by tying them up in red tape 🙂
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