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A thought experiment (answer highly appreciated):
Consider the matrix to be a simulation consisting of at least two levels. Consider ALL participating persons to be sub programs with certain properties (character, intellect, etc). Some of them do have constraining tasks only (a purpose - architect, oracle, agents, sentinels, key maker, merovingian) to define 'the world that is'.
Commons ("real people", but programs anyway) are almost entirely spawned in Level 1. It is a 'survival of the fittest' level, which is completed by staying alive after discovering that a conspiration exists. That includes, that from the very moment 'you the program' discover the traces of the matrix, you are immune to be replaced by an agent (or why else wasn't Neo simply replaced when searched after at the beginning of Matrix?). This immunity is given by the matrix itself, it's a constraint of Level 1.
Level 2 common programs (advanced from Level 1 or "born" in Level 2 - inheritance!) are in a position to elect common level 1 programs to advance to Level 2. The promotion of the candidate is dependend on the choice of whether he wants to stay in Level 1 only (and forget) or advance to Level 2. He is only then given god-like mode in Level 1, but concerning the rules of the game he still can die there and die in level 2 in the same instant. One dies very easily in Level 2, which instantly removes one from level 1. Hence the degree of difficulty is enhanced, which is supported by the fact, that even if you are nearly god in Level 1, you need to have friendly programs securing your helpless residual in Level 2. You have to rely on others, that's for sure.
Now, what is going on at the end of Reloaded? Level 2 Neo is as secured as he can possibly be. Level 1 Neo operates as a god, but needs the help of friendly programs (Morpheus, Trinity, etc.) in BOTH LEVELS to reach the point of choice for LEVEL 3. The options are to remain in Level 2 (rebuilding Zion) or to advance to the next Level (by choosing Trinity). Level 3 Doors are like Level 2 Pills.
Neo chooses right, by what we can see now. How can I tell? To affect reality in Level 1 one has to advance to Level 2 before. To change reality in Level 2 one pretty likely has to advance to Level 3. That does not necessarily mean there is a whole third level in a physical sense.
To explain that thought: The architects room "is situated" in Level 1, but cannot be reached by anyone (except the choosen one). So for all other programs of Level 1 (and 2?) it is NOT connected to their Level. It is a separated level, a region of safety for the residual of Neo. But he (like the oracle) is still subject to complete erasure when killed in one of the physical Levels.
Neo (the son) could now possibly operate at the same level as the architect (father) or the oracle (mother) do - he was now "adult". Likewise Neo could have to explore another 21 Levels to reach the architects level. Who knows?
But forget about the story arc of Level 2, it most likely exists only within the matrix. It may even occur, there is no sensible Reality(TM) outside the matrix, for if you are a mere program, how would you sense the computer hosting your universe? To me that would make a really cool ending...
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