The Machine War is a major event in the continuity of The Matrix franchise. Towards the end of the Second Renaissance, all-out warfare broke out across the Earth between humanity and the artificially-intelligent Machines of 01. In the war's early days, humanity suffers a crushing defeat and is utterly enslaved by its own creations, used as organic batteries to fuel the Machines while at the same time allowed to exist in a computer-generated world known as the Matrix.
History of the war[]
First strike[]
Towards the end of the Second Renaissance, the global economy suffered greatly as a result of the prosperity of 01, leading to a blockade of all trade routes. When the Machines attempted to resolve the situation diplomatically, the world's leaders took great offence and unanimously denied 01's entry into the United Nations, instead choosing to destroy the Machine nation altogether. A nuclear strike was launched against 01, but the Machines were less vulnerable to heat and radiation than humans and so suffered minimal losses. Realising that humanity was unwilling to share the Earth with them, the Machines determined that their survival could only be ensured through dominating their former masters and began invading their surrounding countries.
Operation: Dark Storm[]
Originally, the Machines were powered by solar energy and so the United Nations called for the Earth's skies to be blacked out. The sky was seeded with chemical clouds that blocked the rays of the sun, cutting the Machines off from their primary power source. This action would result in the ruination of the planet's ecosystem and would ultimately prove to be a futile gesture; the Machines had enough reserve energy to continue fighting until they researched a replacement fuel source, which ultimately would be the human race itself.
The first Matrix[]
After mankind suffered a crushing defeat, the Machines focused on utilizing the bio-electric energy generated by the human body, developing a new system to efficiently harvest and renew their new fuel source. The Machines also developed a suitable environment for their human crops, creating a virtual reality system to sustain the human mind and thus forming a symbiotic relationship with their former oppressors. This virtual reality would become known as the Matrix.
Initially, the Matrix was designed to be an idyllic environment where humans could live happily without struggle or suffering. However, the human mind was incapable of accepting such a stagnant state of existence and countless human batteries perished, so the Machines were forced to re-design the system. The Matrix was reconfigured into a replication of society during the late 20th century and the Machines' human charges were able to accept the program for a time. By this point, almost no free humans remained and virtually the entire human race was plugged into the Matrix. It is unknown how long this period of absolute dominance lasted.
The One[]
Roughly 100 years before the war's conclusion, an individual was born within the Matrix who was capable of seeing the system for what it truly was. Not only that, but this figure was capable of altering the virtual environment of the Matrix at will and freed many humans, allowing them to establish the city of Zion near the Earth's core. After this "One" died, an exile program within the Matrix known as the Oracle foretold his return and that his coming would lead to the end of humanity's subjugation.
After the founding of Zion, the Machines took steps to enhance the Matrix to prevent the loss of more human crops. They now faced a renewed outside threat from Zion and became determined to destroy it. The next 100 years would see a bitter war being waged between Zion and the Machines.
Neo[]
The search for the One would ultimately lead to the identification of Thomas A. Anderson, a Matrix resident who also went by the hacker alias "Neo". Neo was semi-aware of the falsehood of the world around him and so was targeted by Morpheus to be offered the choice of discovering the true nature of the Matrix. Neo accepted Morpheus' offer and was released from the Matrix, removed from his Pod by a Docbot and disposed of in the sewers, where he is then retrieved by Morpheus' crew.
Some time after learning the truth about the world and the prophecy of the One, Neo officially joins the Resistance against the Machines and is taken to see the Oracle, an Exile program that provides insight and wisdom to "redpills" opposing the system. The Oracle allows Neo to believe that Morpheus made a mistake in choosing him, that he is not really the One, but she really only tells Neo what he needs to hear, in order to inspire him to walk the path he eventually chooses.
In a confrontation with the Matrix's Agents, Neo is supposedly killed. However, he rises again after being kissed in the real world by Trinity, one of Morpheus' crew. Upon his resurrection, Neo sees the Matrix as programming code, understanding and perceiving its true nature. The Agents fire on Neo, who blocks their shots with telekinesis. Agent Smith then attacks Neo head on but Neo is able to block and parry all of Smith's punches seemingly without even trying. Neo then appears to jump into Smith's form and destroy him from within.
Neo had become the One.
War's end[]
In The Matrix Reloaded and The Matrix Revolutions, the Matrix is threatened from within by Smith, who somehow returned after his destruction at Neo's hands. Now able to copy himself, Smith uses his newfound power and sense of purpose to infect the "bluepills" residing within the Matrix, imprinting himself on their digital personae. By doing this, Smith spreads across the Matrix like a virus, threatening humanity and Machines alike. Neo is told by the Oracle that Smith has essentially become Neo's polar opposite - the "Zero", so to speak - and seeks to destroy not only the Matrix but the real world too.
At the end of Revolutions, Neo and Smith meet one last time to determine the fate of humans and Machines. The Machines have allowed Neo to re-enter the Matrix to battle Smith and destroy him before he overruns their central programming, and Neo asks that the Machines cease their war against Zion in return. When Neo jacks into the Matrix again, he finds that Smith has completely taken control; every bluepill and program across the entire Matrix has been turned into a Smith copy. Neo fights against the leading Smith while the others watch and Neo manages to defeat Smith by letting him imprint himself onto Neo. By doing this, Smith seals his own doom as his essence and Neo's cancel one another out, causing all of the Smiths across the Matrix to explode. With Neo and Smith destroyed, the Matrix can be reformatted and those who wish to be freed from the system are allowed to go.