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In the first movie, Neo destroyed Agent Smith by "entering" his body, literally exploding the code that was Smith from within. When Neo entered Smith, human genetics and machine code combined - allowing Neo to have new powers within the Matrix, and Agent Smith to make a choice not to return to the machines.
So what we have here is the logical culmination of the basis for the 3 films - there are three worlds - the Machine world, the Human World, and the Matrix world. The Machines and Humans believe they cannot live in peace, but we have a showdown between Neo and Agent Smith - two sides of a coin, good and evil, and the triumph of Neo allows Humans and Machines to live peacefully together.
M achine + A gent (Matrix) + N eo = MAN
Neo's human abilities are enhanced by the machine code he receives from the Agent, but his basic humanity triumphs over the cold logic of the code. Agent Smith's machine code is enhanced by the genetic material he receives from Neo, bu this basic machine code cannot ultimately defeat a world of choice and imperfection. That's why in the ultimate showdown, Smith self-destructs when he attempts to assimilate Neo - Neo the Human, enhanced by Machine Code is assisted by the Machines to finally and totally destroy Smith, the out of control Virus.
Most humans will not have Neo's powers, and most programs will not want to live within the Matrix; but thos Humans and Programs that wish to "awake" wil be given the opportunity - Humans in Zion, programs in the Matrix.
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