I was going to write a long story about me interpretation but I saw that Cliffy already did it.
I think you nailed it.
This is known as Ken and Andrew’s Rule of Plot Holes:
My whole problem with the second and (especially) third movies was the substitution of new characters we don’t care about and incomprehensible plots for actually answering some questions. Like, how Neo can stop the sentinels at the end of Reloaded, or what happened to the twins. Instead, in Revolutions, we get what amounts to a war movie with extended battle scenes, and the Neo/Morpheus/Trinity “trinity” is reduced to a sub-plot. They were what made the first movie likeable, not the generals and scrappy youngsters we get in the second two movies. But I’ll stop the bitching hijack now.
Note that “pod-born” humans seemed to have a slightly lower status than “100%natural born humans” as well.
Really nothing the machines say can be considered “reliable” since it is all designed to influence the humans. I would imagine that a machine would not really care one way or the other about things like “honesty” or whatever.
Oracle “So you will keep your word [regarding the truce]”
Architect “What do you think I am, human?”
Which can be read two different ways:
- Humans are subject to breaking their word. Machines aren’t
or - Keeping your word and honor are human concepts. Machines will keep their word so long as it logically makes sense to do so
Also, what is the nature of the Oracle’s precogniscients? Is it just that she is capable of predicting most likely outcomes of events based on whatever info she has? Kind of like a chess computer thining 20 moves ahead. Which would explain why she can’t see past “choices she can’t understand”.
Building on av8rmike’s comment, I don’t think that Cliffy’s theory explains the movies all that well. Assuming that Zion etc. is the “real” world, how does Neo stop the Sentinels in the second movie? He holds up his hand and a bunch of “real” robots just fall to the ground.
Just a note: the Matrix Online MMOG is supposed to continue the story, and perhaps give us more answers.
Except that there is nothing in that dialogue that the viewer needs to construct, suppositions or otherwise, to make sense of what has happened. In other words, what is the plot hole (as it relates to the information in that scene)? Poor explanation/writing and poor directing (which I’m not going to waste time arguing since that I find it impossible to change anyone’s mind on a msg board) should not be confused with actual missing/contradictory plot.
Neo stops the Sentinels because he is connected to the Source. That is, he can influence the Source with his mind. The Oracle explains this to him after Neo is retrieved from the tunnel.
So what’s the Source then? The master computer program (operating system) for the Matrix? I’m completely lost. This means that the computer programs inside the matrix control the machine world?
And Neo connects with this computer program via telepathy?
Mind you, I’m not a programmer, but what I know of programming is that all programs are, in some way, derived (or as some state so boldly, “copied”) from another. That is, each application (or software) is built from/on top another, e.g. see Windows vs. Mac OS. The Source, then, is the basic program that all other Matrix programs are derived from. I’m not so sure that the Matrix controls the machine world. I still think it is quite the opposite. The Machine world (city) was created first. When they beat the humans, the Machines created the Matrix to house the humans. The Machines needed programs to run the Matrix (agents, birds flying, sunrise and sunsets, etc.) Those programs were created from the Source (in the Machine city) and sent to the Matrix to exist.
How does Neo control the Source? There is no clear answer. Not necessarily a plot hole, just like “combined with a form of fusion” is not a plot hole, c.f. no one complained about how the Force worked before, right (Phantom Menance notwithstanding)? Anyway, my theory is that Neo left an implant of himself on the Source when he touched it. He was supposed to touch it (and not survive, apparently) when he met the Architect, but he didn’t choose the (for lack of a better word) “right” door. But, he did touch it, “cause and effect,” the Merovingian might say. In the game, Enter the Matrix, we learn that Neo’s mind (id, self, etc.) is stuck between worlds. That sort of lends to the notion that Neo’s mind is at the Source. Also, he is The One after all.
One must ask what the is point of a machine world without humans.
In the Animatrix - Second Renaissance, they talk about some kind of economic collapse caused because the machine city ‘01’ could produce so much more efficiently than human cities. This begs the question - why did 01 need to create products that humans would want to trade?
I disagree entirely. In order to have drama, we have to have a plausible reason to feel dramatic tension. If those reasons are ludicrous, it’s hard to have any tension, isn’t it?
The problem isn’t so much the attempt to show a reversal - machines becoming dependent on humans - but it was the fact that this reversal was shown in such a clumsy, awkward, and brainless manner. It’s lazy storytelling, plain and simple.
This is my problem with the second and third movies. I borrowed my brother’s Matrix collection awhile ago and watched everything except The Matrix Experience (a three-disc explanation of the movies). When I asked my brother about certain scenes in Reloaded and Revolutions, he told me to watch the explanatory discs and it would all make sense. I shouldn’t have to watch the other discs! If you need to create 10 hours of additional footage to explain what you were trying to say, then you didn’t do your job as a filmmaker.
There was too much to fit in even three movies, and American moviegoers are really not prepared to watch films any longer than that. Bollywood movies tend to be 3 hours long, as a comparison.
Is it a coincidence that “source” rhymes with “force”, the same reason that Dante gave Randall for all the plot holes in Star Wars? 
The guy at matrix-explained.com seems particularly upset about this point.
Myself, I figured Neo must have somehow acquired a wireless connection to the Matrix at some point. It angers me that the 2nd and 3rd movies could have had as much eye candy, but still have answered some questions coherently, been better directed, and have a more satisfying ending. They could have been so much better with just even some minor tweaking, but it’s almost as if the Wachowskis consciously decided against it:
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“Let’s have the last battle be fought in the sky… but instead of a flying Superman II-esque battle, we’ll just have them float next to each other and do their kung fu moves.”
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“Let’s toss in a line about the Keymaker being obsolete by the Agents, despite the fact that he’s obviously still the only way to get to the Source.”
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“Let’s have the machines make an uneasy truce with the humans because of the amazing threat that Smith has become without showing that he’s become a major threat!”
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“Let’s leave everyone confused at the end so that it will make people think that we actually knew what was going on the whole time, so that they can spend endless hours debating things on those silly message board thingies.”
Bah. Show me something new. Show me character motivations. Show me plot connections. Show me intelligent design, for goodness sake, and maybe I’ll respect you in the morning.
So how does Neo’s connection with the Source enable him to stop the Sentinels (huge robotic war machines) in the “real” world, if programs in the Matrix don’t control the machine world?
The idea that the Second Renaissance part one and two left me with made me really want a completely set of different movies than what was given.
I wanted to journey down the rabbit hole. I wanted to look into, around and through the Allegory of the Cave.
I didn’t want a lame high school treatsie on free will.
I figured from the Animatrix that Zion was actually a Second Matrix that offered humanity what they needed, rather than the Matrix which gave them what they wanted. Zion, the mother Source with all the symolism that goes along with that, and the Source, the father god and all of that baggage as well, are having a fight not over batteries or free will. Rather, the battle was over freedom and reality.
I figured the Earth was just fine, bunnies and deer and all. But Zion and Source were trying to decide how to stop humanities foolishness. One used them for processing power. One used them for electrical power. Creativity versus Generativity, almost Utopian Smurfdom versus Utopian Capitalism.
The other idea was they were all in a generation ship and people started waking up so the AI had to figure out some way, any freaking way to keep them asleep.
The fact that the stuff that the fans WANTED was so much more ambitious and impressive than what was shown indicates the failing of the movies. We’re left with an impressive freeway chase and lots of black leather.
Personally, I would have been fine with better action. I liked the first one because it was an exceptionally good action movie; if I wanted philosophy, I would’ve gone somewhere else. The Wachowski brothers ain’t exactly Akira Kurosawa, you know? I could tolerate the silly stoner philosophy of the first movie, but when the filmmakers decided to take themselves too seriously and try to provide answers when they weren’t even capable of asking questions, it ruined the films. I didn’t need to sit through a twenty-minute exposition on free will by someone who failed Philosophy 101.