As we learn in M2 during the conversation between Neo and the Oracle, the Source is the machine mainframe. Beyond this, we are given additional clues about its nature:
In addition to the Earth that zooms away from Neo when Neo is absorbed into the doorway of light, there are actually three quotes that tell us the Source is not inside the Matrix:
Oracle: "...a program can either choose to hide here, or return to The Source."
Neo: "The machine mainframe."
Oracle: "Where you must go."
(The word "machine" indicates an entity in Machine World, not in the Matrix.)
"The door to your right leads to the Source, and the salvation of Zion. The door to your left leads back to the Matrix, to her and to the end of your species." - Architect (M2)
"The power of the One extends beyond this world [the world of the Matrix]. It reaches from here all the way back to where it came from... The Source." - The Oracle (M3)
Not only that, but logic alone tells us that the Source cannot be located inside the Matrix. The Architect had to have some way of coding the first Matrix without actually being in the Matrix.
Neo defeated Smith in the end because Neo was connected to the Source when Smith copied over Neo (more on this later in the Smith: Smith's Defeat page). But where exactly was Neo plugged in? Was he plugged into Deus Ex Machina? Was he plugged into some other machine that behaves as a kind of "wireless router" to connect Neo to the Source? Or does "the Source" merely refer to any place outside of the Matrix within Machine City, where a program can be viewed, upgraded or deleted?
We don't know, but we do know that the Source can go anywhere in Machine City since it apparently came to the random location that Neo arrived at within Machine City. Since Neo (and all machines) are able to connect to the Source wirelessly, it isn't hard to believe that the Source can be accessed from anywhere within Machine City. It could also be that Deus Ex Machina itself is the Source.
When a program is being used by its operating system, it cannot be deleted. For example, if you try to delete an MP3 file while you're listening to it, you get an error because the file is currently in use. It isn’t that your computer is incapable of deleting the file – it’s just a safety net to prevent errors. It is a rule that your operating system has been programmed to follow. If you actually were able to delete the file while listening to it, the MP3 player program would crash at best, and at worst it would crash the entire system and you’d have to restart your computer.
Similarly, it makes sense that a program in the Matrix must first return to the Source (a location outside the Matrix) before it can be deleted, because if it is running around in the Matrix, that means the Matrix itself currently has the program “loaded” into memory. Deleting it while it’s running would certainly result in serious errors within the Matrix, especially considering the fact that humans themselves provide the memory and calculation power for the Matrix. Once in the Source, technically it could be deleted, except the Matrix operates on an additional rule that Microsoft Windows doesn't: programs can choose not to be deleted if they wish to continue running.
I am thankful that Microsoft doesn't give programs a choice to continue running or not – what a nightmare computer operation would become! Likewise, the Architect hates the whole "choice" model despite that it functions. If you and I would become frustrated from having to allow our own computer software to "choose" its own fate, imagine how much this would bother the machine of ultimate mathematical precision, the Architect, in a system jillions of times more elaborate than our own desktop PCs.
Also, in computer science, "source code" refers to the text that a computer programmer writes in order to produce a program. The programmer then uses a compiler program to turn the source code into a program, which means the program is translated from human coding language into machine language. There is no doubt that the Wachowskis were aware of this when deciding what to call the place where Matrix programs are created, modified and deleted.
While Neo's powers inside the Matrix come from the fact that he is a summation of all forms of Matrix rejection, Neo's powers outside of the Matrix come from the Source, as the Oracle says in M3 (above). As I discussed in the Matrix System: The One page, the One probably needs these powers to help free the first 23 Zionists. How Neo's powers actually work will be discussed in detail later in the Neo's Powers page.
In M2, the Keymaker says, "Only The One can open the door [to the Source]...". If we take the Keymaker literally, it means no other human or program can open this door. It's easy enough to understand why no other human can open the door. The main purpose of the Source is to create, modify and delete programs, and Neo is the only human given purpose within the Matrix. Therefore, he is the only human whos code would ever need to be modified or deleted.
As for programs not being able to open the door, this must mean that programs enter the Source differently, because we know that all programs are supposed to return to the Source when it is time for them to be deleted. This makes sense anyway, because it would be hard to believe that a power plant would need to be destroyed and emergency backup power disabled for 27 city blocks every time a program returns to the Source to be deleted.
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