Frey is in cyberspace stealing government documents! Near the end, the glitchy text says Zero Day, which is a type of computer exploit that has yet to be discovered or fixed by the masses. This allows Frey to go undetected by the antivirus programs because the pattern of his attack isn't in the antivirus data base yet.
The quote "Bodies upon the Gears" is from Mario Savio's speech during the Free Speech Movement in 1964 at UC Berkeley (which happens to be where I went for college.)
This is like that mission in Mass Effect 3.. where Shepard has to go to the Geth Consensus, where the network is resembled by a city-like environment in order to be understood by the human mind... I love how you resembled it in this one..