It was already mentioned that the technology to upload mind to a matrix like world exists (and was created by the old man, or at least based on his research), and all of humanity used it. Many (or maybe all) of the people in that virtual fake city lived in the real world in the past (possibly a long time ago since time in the virtual world isn't the same as in the real world) and got there using this tech. It's also why the specialist powers all deal with the mind, since it's all just data in the matrix.
In the same way they can upload the mind to an artificial body in the real world (in this case Inaba's body, who might be a normal AI in the first place and not just a human mind uploaded). Basically Makoto's mind exited the matrix and entered a robot/artificial human body in the real world (which is why the chapter is called transference, as in data/mind transference).