-Wallpapers de la Preview de Android M lanzada hoy en el Google I/O, extraidas de la imagen de la ROM preview
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 Smith said that Humans rebelled at the ‘perfect’ matrix originally made for them.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.