Surreal game.. heres my take on the story: The scientists obviously can't accept the way the government plans to use SGDS, and plan to stand up against Field. Not much they can do though, but Jerry manages to insert a bug into the system (Jerryslittlemonkey made me smile), which prevents manual mode from activating properly; and SGDS's consciousness is trapped within itself, and its memories are damaged, but it still retains the power to shut itself down, if only it can figure out how.
And the walls are the government's people frantically trying to stop it from doing exactly that, while they try to fix the bug. Anyway 5/5! :)