We find out that all of the humans are still in the Matrix. The Architect and Agent Smith both mention that the Matrix is an imperfect environment. Smith said that Humans rebelled at the ‘perfect’ matrix originally made for them. It turns out that the ‘perfect’ world is in fact the matrix that we’ve seen in the first three movies. It was never disassembled. The Zion level was created entirely for those minds that couldn’t handle the main level of the matrix. People like Neo and Morpheus who could see the glitches inherent in any large virtual world. The Zion level simply gave their mind an excuse to brush off any other inconsistencies they might notice.
This answers many of the lingering issues with the first three films. Neo can control the sentries in the Zion level because they are still imaginary constructs within the machine he is attached to. It explains Zion itself, a city with an extremely high level of technology, considering it’s populated by refugees. It also explains the Nebuchadnezzar and the other craft that seems to operate outside the realm of established physics. While they showed similar hovercraft in the Animatrix, these could be explained away as being implanted memories. Implanted memories would also explain why nobody seemed to recall Zion being destroyed and rebuilt over and over.
It would explain the basic flawed premise of the Zion level itself: The machines would need to supply a huge amount of energy to keep the humans alive, rather than use them as a power source as the Zionists believe. Even the evacuation tubes used to discard of humans that ‘wake up’ seem out of place. Why wouldn’t the machines simply recycle the body of anyone unplugged, instead of handing them over to the Zionists alive? It explains how Smith was able to enter the body of an actual human in the Zion level. We know that Smith is basically a virus, hijacking whatever body is convenient. Hijacking is a very common practice in the matrix level, and Smith seemed adept enough to jump levels. We know there was an error in his programming that allowed him to multiply. Apparently the same error allowed him to jump out of his designated environment.
If you’ll remember, Cypher met with Smith. Cypher kept talking about how great the Matrix was to him. The food, the lifestyle were so enticing, so perfect, he was willing to betray his comrades to permanently relocate there, in his perfect world. The extra level also explains how cypher was able to get in and out of the matrix by himself. Remember that he was so good that he was mistaken for "the one" at one point. Apparently he has the ability to exit the matrix level at will.
So the story picks up with all of humanity waking up into a desolate world. There isn’t enough food, shelter, really anything to go around. Riots break out everywhere. Ninety nine percent of the populace doesn’t care about so- called freedom, and they all want back in to the matrix. The Zionists are unable to get control of anything, and Neo faces a real crisis of Conscience. He alone re-enters the matrix in order to seek out the Architect and the Oracle, partly to ask their advice, partly to get away from everyone. He finds the Architect, but is unable to locate the Oracle. Smith arrives on the scene, though with no humans to hijack he is pretty ephemeral. Because he wants a body back, he lets Neo in on the Big Secret: Neo and Morpheus broke the Matrix (with no small amount of help from Smith Himself) and now everyone is being forced to live on Zion level because the damage is too widespread to fix properly.
Neo jumps out to Zion level, where he soon finds the Oracle and learns he can indeed still fly and control things as if he was in the Matrix. What’s more, he is able to grant this power to others. It seems the Machines aren’t as interested in keeping this reality solid. Neo and his troupe learn that the machines are indeed willing to exist on a more limited level , and have plans on killing every human in existence.
Knowing that Neo is at the heart of this newest catastrophe, the Sentries and other assorted dangers try to take Neo out. During the first movie, the Agents tried to shoot Neo in the Matrix level in order to kill him. Despite all the talk given to the rules of the matrix, it still seems a pretty convoluted way to kill someone. This time, He feels lighting going through him, and through sheer force of will he again keeps himself alive. It seems the machines are trying to kill him again, this time forever, but Neo is actually able to mentally stop them from throwing the switch. Reality starts to bend and distort as the machines do more and more to try and stop him. What safety protocols existed are giving way to 'root level' attempts to patch the matrix. Neo starts to level jump at will, being chased all the while by various enemies. He jumps to yet another white room, a level unto itself.
It is at this point that Neo is finally able to break out into meatspace for real. He is the first human in centuries to actually wake up. He finds himself in a huge warehouse, still underground but nothing like the lightning towers shown in the first film. The maintenance machinery has no idea what to do with him, and he is able to finally escape. He gets to the surface, and feels the real Sun on his face for the first time. Aside from massive domes dotting the land, nature has reclaimed the planet. Presently, a robot emerges from the dome he has exited. It is humanoid, but looks like it has not been used in a very long time.
It tells him that he has won. While the machines did not want him to wake up, It is not the intention of robots to destroy the humans, and perhaps now it is time to try to again live together. While they allowed wholesale brainwashing within the matrix, The robot says they cannot kill their creators, and if the matrix universe won’t work, then so be it. At this point we see the inside of the nearest dome, where pod after pod shows signs to waking up. The humans are being released. One by one they stumble into the light, using the pod covers as togas (PG13, of course) The robot says goodbye, good luck, then powers down. Our view rises into the sky, as we see dozens of domes, with people coming out of all of them. We rise higher and higher still, through the clouds and into space, until we come to see a vast orbiting spacecraft. Lights are coming on, engines are beginning to glow, and the craft is slowly sliding out of orbit. Our view zooms into the craft, through several bulkheads, into a huge interior filled with a singe massive computer. We zoom into the computer, down to the chips and circuits, until we see the familiar green cascading language of the original matrix. The Architect steps into view, slowly becoming more and more mechanical. He is greeted by another android. It seems that the robots have been building their own matrix in space. This makes sense considering that the only reason the first robots existed was to serve us in Meatspace.
The Android asks the Architect if everything went according to plan. He says that we emerged earlier than was optimal, earlier than was planned, but that there are adequate food stocks in the domes for us until we get on our feet, and enough processed metals and materials to get humans on the road to civilization in short time. He also mentions that the climate engineering efforts have gotten the planet on a more secure footing for our re-introduction. It seems that far from enslaving us for these many years, the mechanical populace decided to protect us from ourselves until they could get the planet to recover. Now that we are back out in the real world, they are leaving Earth. Robots never needed a planet in the first place, and most robotic minds were simply uploaded into the mecha-matrix. The other Android, the ‘pilot’ says they are stopping at an asteroid for supplies, then heading into orbit around an outer planet, safe from solar fluctuations. From there they’ll keep an eye on humans, in case they are needed to help their creators again.
Neo jumps out to Zion level, where he soon finds the Oracle and learns he can indeed still fly and control things as if he was in the Matrix. What’s more, he is able to grant this power to others. It seems the Machines aren’t as interested in keeping this reality solid. Neo and his troupe learn that the machines are indeed willing to exist on a more limited level , and have plans on killing every human in existence.
Knowing that Neo is at the heart of this newest catastrophe, the Sentries and other assorted dangers try to take Neo out. During the first movie, the Agents tried to shoot Neo in the Matrix level in order to kill him. Despite all the talk given to the rules of the matrix, it still seems a pretty convoluted way to kill someone. This time, He feels lighting going through him, and through sheer force of will he again keeps himself alive. It seems the machines are trying to kill him again, this time forever, but Neo is actually able to mentally stop them from throwing the switch. Reality starts to bend and distort as the machines do more and more to try and stop him. What safety protocols existed are giving way to 'root level' attempts to patch the matrix. Neo starts to level jump at will, being chased all the while by various enemies. He jumps to yet another white room, a level unto itself.
It is at this point that Neo is finally able to break out into meatspace for real. He is the first human in centuries to actually wake up. He finds himself in a huge warehouse, still underground but nothing like the lightning towers shown in the first film. The maintenance machinery has no idea what to do with him, and he is able to finally escape. He gets to the surface, and feels the real Sun on his face for the first time. Aside from massive domes dotting the land, nature has reclaimed the planet. Presently, a robot emerges from the dome he has exited. It is humanoid, but looks like it has not been used in a very long time.
It tells him that he has won. While the machines did not want him to wake up, It is not the intention of robots to destroy the humans, and perhaps now it is time to try to again live together. While they allowed wholesale brainwashing within the matrix, The robot says they cannot kill their creators, and if the matrix universe won’t work, then so be it. At this point we see the inside of the nearest dome, where pod after pod shows signs to waking up. The humans are being released. One by one they stumble into the light, using the pod covers as togas (PG13, of course) The robot says goodbye, good luck, then powers down. Our view rises into the sky, as we see dozens of domes, with people coming out of all of them. We rise higher and higher still, through the clouds and into space, until we come to see a vast orbiting spacecraft. Lights are coming on, engines are beginning to glow, and the craft is slowly sliding out of orbit. Our view zooms into the craft, through several bulkheads, into a huge interior filled with a singe massive computer. We zoom into the computer, down to the chips and circuits, until we see the familiar green cascading language of the original matrix. The Architect steps into view, slowly becoming more and more mechanical. He is greeted by another android. It seems that the robots have been building their own matrix in space. This makes sense considering that the only reason the first robots existed was to serve us in Meatspace.
The Android asks the Architect if everything went according to plan. He says that we emerged earlier than was optimal, earlier than was planned, but that there are adequate food stocks in the domes for us until we get on our feet, and enough processed metals and materials to get humans on the road to civilization in short time. He also mentions that the climate engineering efforts have gotten the planet on a more secure footing for our re-introduction. It seems that far from enslaving us for these many years, the mechanical populace decided to protect us from ourselves until they could get the planet to recover. Now that we are back out in the real world, they are leaving Earth. Robots never needed a planet in the first place, and most robotic minds were simply uploaded into the mecha-matrix. The other Android, the ‘pilot’ says they are stopping at an asteroid for supplies, then heading into orbit around an outer planet, safe from solar fluctuations. From there they’ll keep an eye on humans, in case they are needed to help their creators again.
