"It's only a piece of the Matrix, at best," said Trinity, watching the hologram and recognizing the bits of coding that she could catch. "Or more like a reflection.

"As you can see, it's based on a system separate from yours. Its purpose isn't to interfere with your programming, but to cut off the programming that's blinding you." Much like the program, the red pill, that they used for humans. Same idea, different execution.