Disclaimer: First of all I hate disclaimers and second of all I don't own the Matrix or any of it's charchters just this story.
Smith has knocked Neo out of the sky and into a huge hole created by the fall. But even though he's hurt Neo starts to get up.
"Why, Mr. Anderson? Why? Why? What are you doing? Why get up? Why keep fighting? Do you think you're fighting for something? Something worth more than your survival? Can you tell me what it is? Do you even know? Is it for freedom or truth? Perhaps peace, or could it be for love? Illusions Mr. Anderson. The effects of a feeble human intellect, trying desperately to justify an existence that is without meaning or purpose! And all of them as artificial as the Matrix itself! Although only a human mind could invent something as insipid as love. So why, Mr. Anderson? Why? Why!? Why!? Why do you persist!? said Agent Smith
"Because I choose to." Said Neo.
Neo punches Smith in the face multiple times then finally punches him so hard he goes flying into and through the dirt wall of the hole. Neo looks up at all of the Agent Smith clones surrounding him and thinks that it is finally over when Smith comes smashing back through the wall and knocks him down again where he lies badly hurt and barely conscious. Smith starts to approach him but stops.
"Wait. . . I've seen this. This is it!? This is the end! I was standing here, right here and you were laying right there and I'm supposed to say something. I'm supposed to say: Everything that has a beginning has an end Neo. Wait a minute this isn't right this can't be right."
Neo gets up and slowly approaches Smith who backs away scared.
"Get away from me!" yelled Smith.
"What are you afraid of," asked Neo.
"It's a trick," yelled Smith.
"You were right Smith, you were always right. It was inevitable," said Neo.
Smith rushes up to Neo and sticks his hand into him and starts turning him into a clone while Neo doesn't try to stop him. Finally Neo is a Smith Clone.
"Is it over?" asked Smith.
The Smith clone that used to be Neo nods.
Meanwhile in the Real World in Machine City the Source takes this opportunity to destroy Smith forever. The Source starts sending a deletion program to Smith using Neo. The Source knew that all of the Smith's are connected and if he distributed a deletion program to the Smith now possessing Neo it would spread to all of them and destroy Smith and return everyone else to normal.
Meanwhile in the Matrix Smith watches as the Smith clone that used to be Neo starts to glow and he realizes what it means as he feels something happening and witnesses all of his clones start to glow.
"Oh no, no, no, no it's not fair," said Smith
Smith can only watch as the deletion program destroys the Smith clone in Neo and causes all of the others to glow. Smith can only scream as the deletion program causes him to glow and then explode finally destroyed forever and then destroy his clones returning them to who they were before they were turned into his clones.
In the Machine City all of the connectors jacking Neo into the Matrix remove themselves from him as he is returned to the Real World.
"It is done," said the Source who then left the scene.
In Zion all of the Sentinels left and once the Kid spread the word everyone began to celebrate.
"Neo, wherever you are thank you," said Niobe while hugging Morpheus.
Like Smith had always said it was inevitable, but now it was inevitable and over.
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