Master Matrix is a powerful computer in Antarctica that "evolved" sometime between 1996 and 2188, and which will serve as the "operating system" for the entire planet; the LXM robots are connected to it and able to tap upon its files containing all human knowledge. It also controls the artificial environments inside the city of New Camelot.  In fact, it may or may not be located in or near New Camelot.
When the Space-Spawn invade Earth in 2198, one of their first actions will be to steal the Matrix, thus rendering the planet paralyzed and easily conquered. 
While the Master Matrix is said to have evolved, it is still entirely a machine.  The Matrix nanotechnology constructed in the late 20th century will have "a lot" to do with the Master Matrix.