This is regarding Kid's Story from Animatrix.
I thought if you died in the Matrix, that you also died in the real world. How did the Kid die in the matrix but not in the real world? Is this somehow related to self substantiation?
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After Kid commits suicide in the Matrix, he wakes in the real world to the following conversation:
Trinity: His vitals are good. He’s gonna make it. Its unbelievable. I didn’t think self-substantiation was possible.
Neo: Apparently it is.
While the process of self-substantiation doesn't appear to be fully documented, the best guess is that Kid's faith in Neo somehow broke his connection to the Matrix, and allowed him to wake up.
Others have self-substantiated through awareness of the Matrix through:
"...a rare degree of intuition, sensitivity, and a questioning nature"
"...some attain this wisdom through wholly different means".