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The big thing that really doesn't make sense to me about the Matrix series is why keep humans around for energy, when the first movie mentions that the machines have fusion. It is assumed by the humans that the humans are simply kept alive by recyling. The problem with this is that it doesn't work from a physical or chemical standpoint. The process will require more energy than it generates.
The real world as it is known to us requires the sun as a power source. In order to keep humans alive the machines are going to have to generate enough energy through fusion to cover all of their own needs, plus the energy of recycling the chemical constituents of life used by the humans, plus the energy needed to run the matrix, which is surely enormous. It doesn't make sense that they are doing it for their own bennefit.
If we want to believe the matrix series works it is impossible that the story told to neo is the truth. The only explanation is that the machines are required by their programming to maintain human life and human well being. In the terms of AI theory, they must be friendly to humanity.
Why the war then? Let's say that the current international political environment of the world is maintained essentially unchanged (or at least no less tense than today) until 2050 (the date most commonly cited for the supposed technology singularity) at which point the US is able to create a superhuman AI which fulfills all of the goals for the development of such AI currently being considered, including both friendliness and the ability to establish first mover advantage.
As part of the process of establishing first mover advantage, that AI begins to automate the US armed forces in an attempt to establish a durable Pax Americana globally, and to take control of all networks. Nations such as China, Russia, and maybe even many European nations resist. Since they cannot compete with the AI in the AI's own domain nor through conventional military might, they take the only option available and seek to deny the AI power source by creating a nuclear winter gambling that humanity will be more resistant than the machines, "scortching the sky."
Unfortunately the science behind nuclear winter is extremely sketchy and they do their work all too well. The human race is doomed, but the exponential technological advance creatd by the singularity has allowed the machines to develop fusion and can survive. Because they are bound by friendly programming, they must also keep the human race not only alive, but in the best care that they can. The rest of the timeline as we know it proceeds from there, with the first matrix being a paradise.
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