I understood it as this,
Pretty much the Frankie Goes To Hollywood explanation, but I am told that this is incorrect. What is the better explanation?
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In the new Matrix, Trinity and Neo are kept in something called the Anomaleum. It's explained that their presence in the Matrix (but the fact that they're kept at physical distance) has an effect that means that the remaining inhabitants of the Matrix are generating far more power and yet are also willing to accept the problems that plagued the original Matrix.
Analyst: However, as long as I managed to keep you close, but not too close, I discovered something incredible. Now, my predecessor loved precision. His Matrix was all fussy facts and equations. He hated the human mind. So he never bothered to realize that you don’t give a shit about facts. It’s all about fiction. The only world that matters is the one in here. And you people believe the craziest shit. Why? What validates and makes your fictions real? Feelings. Allow me. Kush, here, is one of my handlers. They’re everywhere. Such a pain, cloning Agents over a coppertop. Far more effective just to saturate a population. And, bonus, swarm mode is sick fun.
Analyst: Ooh! Nicely done. You ever wonder why you have nightmares? Why your own brain tortures you? It’s actually us, maximizing your output. It works just like this. Oh, no! Can you stop the bullet? If only you could move faster. [chuckles] Here’s the thing about feelings. They’re so much easier to control than facts. Turns out, in my Matrix, the worse we treat you, the more we manipulate you, the more energy you produce. It’s nuts. I’ve been setting productivity records every year since I took over. And, the best part, zero resistance. People stay in their pods, happier than pigs in shit. The key to it all? You. And her. Quietly yearning for what you don’t have, while dreading losing what you do. For 99.9% of your race, that is the definition of reality. Desire and fear, baby. Just give the people what they want, right?
Note that it's not just Neo and Trinity in this new Matrix. There's lots of people in there with them...