After all the nuclear bombs went off, there was this little kid running around and singing. His parents were calling him home, and suddenly, they turned into what looked to me exactly like agents.
What were agents doing in the real world? Did I miss something?

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What? I don't think that was the real world. Otherwise agents wouldn't be in it. Unless something had changed somewhere...

I know it was the real world because we saw the agents put the kid into that pink bath and into the MAtrix

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We did not see the agents put the kid into "the pink bath." We saw a child in the ruins of demolished city playing in the snow. We then saw a different camera angle where the child was playing in the snow and the child begins approaching a house, with a mother and father figure in the doorway. We then saw flashes of agents as the mother and father. We then saw the child scream in horror. We then saw the camera zoom out and show that the child is plugged into the Matrix.

Please note, SR2 directly precedes "Kid's Story" and the child in SR2 has the same physical characteristics, albeit younger, as the child in "Kid's Story."

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Here we are at last!!!

First:did you know that an nuclear bomb generates an EMP???
Second:if Agents are in the real world,that means that all the sequence that have preceeded the explosion is already part of the Matrix illusion...

Well,if a nuclear bomb generates an EMP,how the machines could have survived to 0-1's nuclear bombing???
If machines cannot resist to an EMP,centuries after,how did they manage to survive to those ones generated by the massive nuclear strikes???
Men are so stupid to have darkened the sky on all the Earth's surface???
Wasn't it more accurate to only darken the sky above 0-1 and its surroundings???
0-1 is located in the mid-East where natural energy is abundant,I mean petrol:so why humans would have tried to deprive the machines of Zion of solar energy if there is an abundant and almost available source of energy???
How could the sky stay darkened over centuries???

About the nuclear bombing:machines couldn't have won the war,it is impossible!!!
They lost it and got crushed just like the insect on the wall just where 0-1 is located,before the UN(?) conference...
So where do the images of the Machines' victory over humans come from???
It is a lie...
And the fact that Agents appear in the real world just shows us that all SR2 is in the Matrix illusion...

I think the whole thing with the kid and the agents simply represents the birth of the matrix. If the sky is scorched in the real world, how can it snow?

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the kid wasn't in the Real World, he was in the Matrix the whole time we see him (until we see his pod of course) The boy must of been feeling like Neo did, he is aware that his reality is false and the Agents go to stop the anomaly before he escapes.

The Architect states that the Matrix went through many versions before settling on the final one, maybe one of his first designs (After Eden of course) was an exact copy of what the earth looked like that time.

I think it's all a darn good story

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Exactly what he said the kid was already plugged into the matrix, but I got one question was that like the first matrix (Reloaded talked about 5 other matrixs before 'this' one).

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Coudln't have been the first matrix if Smith was always right as Neo said. What Smith said in the first movie implied that the first matrix wasn't patterned after the twentieth century at all.

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It wasn't, it was a perfect world but humans never accepted it the way that child never accepted being imprisoned and all the crops were lost, Smith and the Architect were telling the truth at that part and the Animatrix proves it, the kid is just a kid he isn't a previous One he was just like everyone else plugged in at that time.