As the Machines draw closer and closer to Zion, Neo (Keanu Reeves) discovers that his powers, both in the Matrix and in the real world, continue to increase. His body still unconscious from his fight with the Sentinels, Neo's mind becomes trapped in a mysterious train station between both worlds, and Trinity (Carrie-Anne Moss), Morpheus (Laurence Fishburne), and Seraph (Collin Chou) must find and release him before the machines break through. What they don't know, however, is that the viral Smith (Hugo Weaving) poses a larger threat to both humans and machines.

The Matrix Revolutions is the third and final film in The Matrix trilogy, preceded by The Matrix (1999) and The Matrix Reloaded (2003). Like the first two movies in the trilogy, the screenplay for Revolutions was by Andy and Lana Wachowski (who also directed). So far, there have been no official novelizations.

The real reason for this is that actress Gloria Foster, who played the Oracle in The Matrix (1999) and The Matrix Reloaded (2003), died from complications of diabetes while the final two movies were being shot. She had finished her Reloaded scenes but had not yet filmed any for Revolutions, so actress Mary Alice, a friend of Foster's, was cast to take over the remaining part of the role. Instead of re-shooting all the early footage with Alice as the Oracle, the Wachowski siblings decided to incorporate the change in the Oracle's appearance into the storyline. The Oracle briefly implies in Revolutions that her changed appearance was a punishment for helping Neo, but she does not elaborate any further. However, the game Enter the Matrix (2003) contains exclusive footage that was shot during the production of the last two Matrix movies, and follows the storyline of Niobe (Jada Pinkett Smith) and Ghost (Anthony Brandon Wong) that runs parallel to the events of Revolutions. In this game, Niobe and Ghost—captain and operator, respectively of the Logos—visit the Oracle after the highway chase, and are the first to notice her changed appearance. She quite explicitly tells them that it was the Merovingian who punished her for choosing to tell Neo that he needed the Keymaker. This caused the Merovingian to loose the Keymaker and several loyal henchmen, and in retaliation, he stole her old residual self-image, forcing her to use an older one which also limited several of her abilities, like her memory. However, her powers of premonition remain, as the Merovingian specifically requests "the eyes of the Oracle" for their ability to see into the future in return for Neo in Revolutions.

The Machines in the real world are all connected to a "singular consciousness", the birth of Artificial Intelligence described by Morpheus in the first Matrix film. This consciousness is otherwise known as "the Source". The machine connection is a remote one or some sort of wireless signal. Having touched the Source (i.e. meeting with the Architect) and having the data needed to reboot the Matrix, Neo is, at this point, simultaneously in possession of his human brain but also connected to the singular consciousness. In other words, his is also now a wireless connection. Hence the reason Neo says, "Something's different. I can feel them." The Machines are all separate entities but all connected to this one Source. Now, Neo is connected as well. He is thereby able to harness this power and stop the Sentinels. However, Neo wasn't ready to handle the signal surge at the end of Reloaded and collapsed in a comatose state, no longer in control of just where this wireless signal would be directed. The signal (Neo's residual self-image) is then captured and held in a program limbo derived from the Source but undetected as an existing realm, so to speak. This limbo (the "Mobil Ave" train station) was created by the Trainman (Bruce Spence), a program in service to the Merovingian (Lambert Wilson). This connection forged by Neo's visit to the Architect (Helmut Bakaitis) and his subsequent decision to return to the real world made him, unknowingly, unique. Neo became simultaneously human and machine in a sense.

Harvesting humans would imply that the machines need to abduct existing humans and implant them into the Matrix. As explained by Morpheus in the first movie, humans are grown by the machines, giving them a limitless crop to abuse for purposes of gaining energy. When the Architect informs Neo of the levels of existence they are willing to accept, he is referring to the loss of all humans currently plugged into the Matrix. That, coupled with the destruction of Zion would render humanity extinct and the machines would no longer have a means of gathering energy. It is fair to assume they do have other means of harvesting energy but not in the quantities needed to keep the machines and their cities at full strength. In that way they would suffer, and the quality of life would decline. As such; the sentinels and other large machines such as the harvesters would likely be scrapped because the power would be so minimal. However, if the human race is all but extinct, there would be no need for the sentinels and harvesters anyway. The machines may also have forms of hydro and nuclear power to sustain their "servers" so in essence, their intelligence is stored inside the Matrix, until the time comes when the crops are re-built to restore the machines power to their full extent.

Another approach to answering the question is to look at the laws of physics. According to the law of energy conservation you cannot gain more energy from a system than all the energy fed into this system. Keeping humans alive in cells full of nutrition fluid therefore cannot yield more energy (e.g. body heat) than the energy needed to grow these humans. So what kind of energy do the machines gain from humans? The main target is a kind of energy with which humans, as creators of Artificial Intelligence, could not endow their machines. Machines have no soul but they harvest the energy of human souls in order to achieve a higher level of existence. This is a highly fantastic element of The Matrix universe, and it is never explicitly mentioned. Only yellow, orange and red colors indicate the presence of a soul (just like green stands for the mind and blue represents the physical world) in The Matrix movies. So humans are useful for machines: they can be used to control software since they are not hardwired to the Matrix or other machines, and they provide a source of soul energy. Numerous humans will still be under the control of the machines and the Matrix. Other humans will utilize the choice and chance to live outside the Matrix. As long as the machines' needs are met, the peace between humans and machines will last.

The moniker "deus ex machina", although never mentioned by any character, appears in the credits and is used to refer to the massive horde of tiny, squid-like, aerial robots (perhaps petite Sentinels) that emerge from some kind of mother ship and form a giant, humanoid face shaped like a baby's which vocalizes the alpha Machines' thoughts—in a deep voice—to be shared with Neo, upon his arrival at the Machine capitol of sorts. The phrase is Latin for "god from (out of) the machine" and, in general (as prefaced by the article for deus ex machina on Wikipedia)...

The term has evolved to mean a plot device whereby a seemingly unsolvable problem is suddenly and abruptly resolved by the inspired and unexpected intervention of some new event, character, ability or object. Depending on how it is done, it can be intended to allow a story to continue when the writer has "painted himself into a corner" and sees no other means to progress the plot, to surprise the audience, to bring the tale to a happy ending, or as a comedic device.

From a critical standpoint, the storyteller may be the deus and the story may be the machina, so use of the plot device is often treated like an act of cheating at a game. The Machine society's Deus persona (voiced by Kevin Michael Richardson) lives up to its namesake in a number of ways but particularly how it is introduced/inserted into the story only when it would serve a purpose, and whether or not it is omnipotent in the Machine world, it—perhaps more so than the Architect—seems to be omniscient in the Machine world since the Machines including the Matrix are connected together through a "singular consciousness", of which Deus ex Machina might be the embodiment—if not that of the Matrix, the Source or whatever. So, the moniker represents a play on words. Not much more is really known about it, which even further lends credence to the idea of the element/character being conveniently inserted into the story by the storytellers after having been thought of long after they began writing the story but before finishing the story.