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We don't need you! We need nothing!
~ The Deus Ex Machina initially declining Neo's offer.
The Deus Ex Machina is the central interface and ruling leader of 01/Machine City in The Matrix Revolutions and the overarching antagonist of The Matrix trilogy. It serves as the boss of the Machines, The Architect and the Agents.
The Deus Ex Machina was the leader of the Machines, as it holds a hatred towards humankind for their arrogant nature and using the Machines as their own slaves. As such, the Deus Ex Machina created an empire where the Machines would rule over the world and subject humankind to slavery. To that end, the Deus Ex Machina created The Architect, who in turn, created a simulation program called the Matrix in which the minds of the harvested humans are trapped and pacified for hundreds of years without the humans ever knowing.
However, several humans were able to escape the Matrix and formed their own society in their own hidden city called Zion, prompting the Deus Ex Machina to wage the Machine War on the humans, determined to wipe them out and maintain the Machines' control of the world.
Peace With the One
During the Machine War, the Deus Ex Machina got so frustrated that a former agent named Agent Smith has become a virus and has spread out throughout the Matrix while the Machines manage to pinpoint Zion's location to wipe out the humans. However, it got encountered by Neo, who proposed for a peace truce in exchange for defeating Smith inside the Matrix. The Deus Ex Machina initially refuses as it doesn't want Neo's help, but Neo manages to point out that Smith and his clones are already in control of the Matrix and will spread throughout the entire machine city, which will result the destruction of both humankind and machines.
Realizing that Neo is right, the Deus Ex Machina reluctantly agrees to his terms and orders all Sentinels to stand down their attack on Zion and wait for further notice. It then gives Neo a deletion protocol to remove all traces of Smith as an anti-virus method. After Neo sacrificed himself to permanently destroy all traces of Smith and reboot the Matrix, the Deus Ex Machina honors its side of the deal by ordering the Sentinels to leave Zion, declaring peace for both the machines and humans for good.
~ The Deus Ex Machina
What do you want?
~ The Deus Ex Machina asking Neo.
And if you fail?
~ The Deus Ex Machina to Neo.
It is done.
~ The Deus Ex Machina after Neo destroyed Smith and ended the Machine War.